We are studying the genetic basis of non-syndromic hearing loss in North Indian population and we performed the PCR-RFLP assay described by authors for the detection of W24X mutation in this article. The assay was carried out using the primers (1F and 1R) and the restriction enzyme Alu1, as described by the authors. However, we have observed a distinctly different RFLP pattern for this mutation as compared...
We are studying the genetic basis of non-syndromic hearing loss in North Indian population and we performed the PCR-RFLP assay described by authors for the detection of W24X mutation in this article. The assay was carried out using the primers (1F and 1R) and the restriction enzyme Alu1, as described by the authors. However, we have observed a distinctly different RFLP pattern for this mutation as compared to that reported by Ramshankar et al, 2003.
The authors have reported that the presence of W24X mutation introduces an Alu1 restriction site. According to them, Alu1 digestion of 286bp PCR amplified product from unaffected subjects produces a single fragment of 286bp, whereas the presence of W24X mutation in homozygous genotype would produce two fragments of 182bp and 104bp and in W24X heterozygotes, it would generate three fragments of 286bp, 182bp and 104bp.
However, we observed that the presence of W24X mutation in homozygous state produced three fragments of 168bp 104bp and 14bp, whereas in W24X heterozygotes we found four fragments of 272bp, 168bp 104bp and 14bp, which suggested that there may be an additional Alu1 site in the 286bp PCR product. An in-silico PCR amplification followed by restriction digestion using REBASE (http://rebase.neb.com) showed that the 286bp fragment amplified by the given primers carries another Alu1 restriction site independent of the one created by the presence of W24X mutation (Fig.1).
Hence, even in the absence of W24X mutation, the Alu1 restriction digestion of 286 amplicon gives two fragments of 272bp and 14bp (Fig.2). Indeed, we have observed these RFLP patterns in control and W24X positive samples. Thus, our results confirm the presence of an additional Alu1 site in the 286bp amplified PCR product giving RFLP pattern different from that reported by these authors.
Figure 1. Alu1 restriction sites in 286bp amplicon (Part of NC_004004).
We read with interest the recent article in the J Med Genet by
Tessier et al.[1] confirming our report[2] of association between
type 1 diabetes and the 2´5´-oligoadenylate synthetase OAS1
antiviral gene. However, their conclusion differs from ours
concerning which single nucleotide polymorphism (SNP) in OAS1
is most likely to produce the functional effect on diabetes
predisposition – the exon 3 non-...
We read with interest the recent article in the J Med Genet by
Tessier et al.[1] confirming our report[2] of association between
type 1 diabetes and the 2´5´-oligoadenylate synthetase OAS1
antiviral gene. However, their conclusion differs from ours
concerning which single nucleotide polymorphism (SNP) in OAS1
is most likely to produce the functional effect on diabetes
predisposition – the exon 3 non-synonymous SNP rs3741981 or
the intron5/exon7 splice site SNP rs10774671.
Since these SNPs are in linkage disequilibrium, determining which is more likely to
be functional is not a simple exercise. We postulated that the splice
site SNP, which as we previously showed[3] creates different
isoforms of the enzyme and is highly significantly associated with
OAS enzyme activity, is the best functional candidate, rather than
the exon 3 SNP which Tessier et al. champion. There were two
reasons for our conclusion:
1) the splice site SNP was more
strongly associated with diabetes in our data than the exon 3 SNP;
2) we clearly demonstrated in our previous study[3] that while
controlling for genetic variation at the exon 3 SNP, the splice site
SNP was still significantly associated with enzyme activity, but the
reverse was not true – there was no association of enzyme activity
with the exon 3 SNP while controlling for genetic variation at the
splice site SNP.
Since the strong effect on antiviral enzyme activity
is a plausible functional link to diabetes susceptibility, these two
observations led us to suggest that the splice site SNP is the most
likely determinant of diabetes predisposition. Tessier et al. found
similar strength of diabetes association for the exon 3 and splice
site SNPs, but further analysis (see below) convinced them that
the
exon 3 SNP was more important. They suggested that the exon 3
SNP could alter dsRNA binding, which is required for enzyme
activation. Hartmann et al.[4] reported that dsRNA binds to OAS1
along an extensive positively-charged groove. There is no
evidence that the GGC(Glycine) to AGC(Serine) substitution
encoded by the exon 3 SNP is within this groove or alters dsRNA
binding.
Nevertheless, it is theoretically possible that some other effect of
OAS1 genetic variation (other than changing enzyme activity)
could also predispose to type 1 diabetes. The question of which
SNPs create functional effects becomes even more pertinent as
further studies reveal new OAS1 associations -- for example, it was
recently reported[5] that susceptibility to SARS virus infection is
significantly associated with both the exon 3 SNP and exon 7 SNP
rs2660 (the latter is in tight linkage disequilibrium with the exon 7
splice site SNP).
Therefore, to directly address the question of
possible effects of the exon 3 SNP on diabetes susceptibility, we
have re-analyzed our data in the same manner as Tessier et al.
They argued that the critical test was to examine transmission of
the haplotype G-A (G allele at the exon 3 SNP and A allele at the
splice site SNP) to diabetic children from parents who were
heterozygous for haplotypes G-A and A-A. Since the G allele is
associated with diabetes at both SNPs, this particular transmission
test would be expected to show overtransmission of G-A to diabetic
children if the exon 3 SNP is functional (as they suggested), but no
overtransmission of G-A if the exon 3 SNP is not functional (as we
postulated). [Note -- in Tessier et al., the major and minor alleles at
the exon 3 SNP are incorrectly called T and C, rather than A and G
as read off the plus strand.]
Tessier et al. observed 50
transmissions and 27 non-transmissions of the G-A haplotype from
G-A/A-A parents, with a corrected p value of 0.03. In our families,
there were 64 parents who were heterozygous G-A/A-A. The G-A
haplotype was transmitted 46 times and not transmitted 52 times to
their 98 diabetic children (difference not significant). These results
do not replicate those of Tessier et al. In fact, when data from the
two studies are combined, 96 transmissions and 79
non-transmissions no longer constitutes significant
overtransmission of the G-A haplotype (chi-squared = 1.65,
uncorrected p = 0.20).
Since this critical test for a functional effect
at the exon 3 SNP fails, we again conclude that the splice site SNP
is the best candidate for the effect on predisposition to type 1
diabetes. Ultimately, biological rather than statistical tests will be
needed to conclusively establish the effects of these OAS1 SNPs
on enzyme activity and other processes such as apoptosis; we are
currently performing such experiments.
In their discussion, Tessier et al. stated they were "puzzled" by the
fact that we found the diabetes relative risk of the OAS1 gene to be
comparable to that of the insulin (INS) gene region. However, we
clearly stated that our relative risks were obtained by comparisons
with unaffected siblings, not with unrelated persons in the general
population, which could alter the relative risks.[2] We suggested
that our OAS1 data supports not only a predisposing effect of
splice site allele G (as also found by Tessier et. al.) but a protective
effect of splice site allele A, particularly in the context of other
diabetes-predisposing genes, since the A allele was found
significantly more often in unaffected siblings than in parental
non-transmitted alleles.[2]
Finally, in their discussion Tessier et al. suggested that there may
be parental-sex-specific OAS1 effects, since the overtransmission
of OAS1 susceptibility alleles was statistically significant from
mothers but not statistically significant from fathers for all three
SNPs examined (note that due to linkage disequilibrium, these are
not independent tests).
However, they did not report whether these
differences between maternal and paternal transmission rates
were statistically significant. Data in their Table 4 shows that there
is also overtransmission of predisposing alleles from fathers but
the effect is not as strong as from mothers; our calculations indicate
that the differences between their maternal and paternal
transmission rates are not significant (data not shown). They also
suggested that mothers of diabetic children may have lower
frequencies of diabetes-predisposing genotypes (GG + GA) than
fathers (p = 0.045 for one of the three SNPs). In our families, we do
not see any significant differences between mothers and fathers in
frequencies of alleles transmitted/non-transmitted to diabetic or
unaffected children, nor any significant differences between
mothers and fathers in frequencies of predisposing genotypes or
alleles (data not shown). Thus, given the available data, we
conclude that there is currently little evidence for OAS1
parental-sex-specific effects on diabetes susceptibility.
Conflicting interests: none declared
References
1. Tessier MC, Qu HQ, Frechette R, Bacot F, Grabs R, Taback SP,
Lawson ML, Kirsch SE, Hudson TJ, Polychronakos C. Type 1
diabetes and the OAS gene cluster: association with splicing
polymorphism or haplotype? J Med Genet Published Online First
13 Jul 2005; doi:10.1136/jmg.2005.035212 [Epub ahead of print]
2. Field LL, Bonnevie-Nielsen V, Pociot F, Lu S, Nielsen TB,
Beck-Nielsen H. OAS1 splice site polymorphism controlling
antiviral enzyme activity influences susceptibility to type 1
diabetes. Diabetes 2005; 54(5):1588-1591.
3. Bonnevie-Nielsen V, Field LL, Lu S, Zheng DJ, Li M, Martensen
PM, Nielsen TB, Beck-Nielsen H, Lau YL, Pociot F. Variation in
antiviral 2',5'-oligoadenylate synthetase (2'5'AS) enzyme activity is
controlled by a single-nucleotide polymorphism at a
splice-acceptor site in the OAS1 gene. Am J Hum Genet 2005;
76(4):623-633.
4. Hartmann R, Justesen J, Sarkar SN, Sen GC, Yee VC. Crystal
structure of the 2-specific and double-stranded RNA-activated
interferon-induced antiviral protein 2-5-oligoadenylate synthetase.
Mol Cell 2003; 12(5):1173-1185.
5. Hamano E, Hijikata M, Itoyama S, Quy T, Phi NC, Long HT, Ha le
D, Ban VV, Matsushita I, Yanai H, Kirikae F, Kirikae T, Kuratsuji T,
Sasazuki T, Keicho N. Polymorphisms of interferon-inducible
genes OAS-1 and MxA associated with SARS in the Vietnamese
population. Biochem Biophys Res Commun 2005;
22;329(4):1234-1239.
In the recently published report "Analysis of RUNX1 Binding Site
and RAPTOR Polymorphisms in Psoriasis: No Evidence for
Association Despite Adequate Power and Evidence for Linkage"[1]
the authors report failure to see association of psoriasis
susceptibility to a region of chromosome 17q25. This region was
first identified with linkage analysis by our group[2], and we recently
reported evidence for a...
In the recently published report "Analysis of RUNX1 Binding Site
and RAPTOR Polymorphisms in Psoriasis: No Evidence for
Association Despite Adequate Power and Evidence for Linkage"[1]
the authors report failure to see association of psoriasis
susceptibility to a region of chromosome 17q25. This region was
first identified with linkage analysis by our group[2], and we recently
reported evidence for association to two unlinked loci from this
chromosomal region.[3] In this instance one associated SNP allele
leads to loss of a putative RUNX binding site. It is important to
address the approach and findings of Stuart et al. (2005)[1] since
they omit important factors that may be required for replicating
associations between genetic loci and complex traits:
1) The statement about adequate power in the title, and the
discussion in the text is misleading. The power these authors
report is only accurate for the parameters they considered. They
fail to consider the inherent heterogeneity of a disease such as
psoriasis and do not incorporate a number of critical parameters
into their power analyses. These include: (i) locus heterogeneity,
(ii) disequilibrium (r2) less than 1.0, (iii) phenotype and/or
genotype misclassification and (iv) the effects and interactions of
environmental risk factors with genetic factors (currently unknown
for complex traits). All are realistic factors and all can substantially
reduce power to detect either linkage and/or association.[4-15]
2) The issue of genetic heterogeneity is of great importance in
complex human disease genetics. It has been demonstrated that
sample size needed to replicate a positive linkage study exceeds,
by a considerable margin, the original sample size, particularly
when factors such as heterogeneity are involved.[16] Effect sizes in
published positive studies tend to be inflated over what one gets
after much more data collection.[17] Such studies are simply more
fortunate with respect to the component of the study that leads to
publication, but it does not mean that they are false positive
results. Since Stuart et al. (2005) did not include heterogeneity into
their power calculations they cannot have addressed this issue.
3) Genotype misclassification seems particularly relevant in this
work. The authors comment that they reconstructed haplotypes
using the methods implemented in Merlin and PHASE (with the
exception of FBAT). This reconstruction was done to address
issues about inflation in type I error due to SNP markers that are
not in linkage equilibrium. However, it has been well documented
that haplotype reconstruction methods such as these are prone to
misclassification18, and that misclassification probabilities may be
large for nuclear families like those studied in this work.[19]
4) It is not clear why the authors did not perform a TDT analysis
using all the affected individuals in the pedigrees, i.e. perform a
linkage analysis with the tightly linked markers? The authors report
that they had 1,285 affected individuals in total. Yet, they chose to
perform an association analysis with TDT, therefore using a
maximum of 351 trios (Table 1), or less than 1/3 of the available
data. The TDT linkage analysis using all affecteds was the
analysis performed in our study[3] and so without a corresponding
analysis on their part, a direct comparison is not possible. It is also
interesting that although the ratios of transmitted to untransmitted
alleles are by no means significant in the study of Stuart et al.
(2005) there is a trend in all pedigrees in the direction we report:
(for SNP9/rs734232 the ratio of the associated A allele in
transmitted versus non-transmitted chromosomes is 235:219).
5) Another issue that could be relevant is the pedigree
ascertainment. Although the ratio of sampled affected to unaffected
individuals in the pedigrees in our study[3] does not appear to be
very different from the same ratio in the pedigrees of Stuart et al.
(2005)[1], there could also be an effect if there is a difference in the
way the pedigrees come to attention in the two studies. It is
possible that the complete pedigrees (including unsampled
individuals) are larger with more affected individuals in the former
study[3] than in the latter.[1] The two samples could then end up with
different fractions of a particular risk haplotype. A comparison of
haplotype frequencies obtained by Stuart et al. (2005)[1] and
Helms et al. (2003)[3] does indeed suggest some systematic
difference between the data sets and/or analyses. Stuart et al.
(2005)[1] state that the combined frequency for the two most common
haplotypes was between .992-.999 for the two regions (depending
somewhat on methods of reconstruction). In the study from Helms
et al. (2003)[3] , the combined frequency of the two most common
haplotypes on non-transmitted chromosomes was 0.94-0.95. This
suggests either that the reconstructions are flawed, or that the
samples differ. The difference could either lead to difference in
power, since if one has more different haplotypes there may be
more informative transmissions. Alternatively it could indicate a
fundamental sampling difference.
6) Given that we report five SNPs driving association in our
families, it is surprising that Stuart et al. (2005)[1] did not attempt to
examine the haplotypes determined by more than just three
associated SNPs. As we report, in a case/control study, evidence
for association with associated haplotypes demarcated by these
five driving SNPs was greater than with single SNPs.[3]
7) Stuart et al. (2005)[1] also state that "only one marker in this
peak
exceeded the p=0.05 level of significance after the most stringent
level of correction for multiple testing", making independent
confirmation critical. However, our level of correction for multiple
testing employed the FDR method[20,21], because employing a
Bonferroni correction for association studies with multiple SNPs is
considered excessively conservative, generally obliterating any
signal in large-scale associations studies. With the FDR method,
nine markers in the SLC9A3R1/NAT9 remained significant. There
are several other studies reporting that adjusting for multiple
testing in studies is less important than other concerns.[22,23]
8) A final general comment is warranted. We believe that
chromosome 17q25 may harbor a number of loci for psoriasis
susceptibility. The issue of clustering of genes for complex traits
has been reported by others[24,25], and is thought to facilitate
identification of susceptibility loci with linkage analyses. Stuart et
al. (2005) also see linkage of psoriasis to 17q25, in a region
harboring the putative RUNX site downstream from SLC9A3R1/
NAT9 and in a region distinct from that seen in two independent
studies of large multiplex families[2,26], but where we also see
linkage in our large set of nuclear families.[3] Previous studies with
simulation data suggest that single major gene analysis of
complex traits has good power to localize genes to a specific
chromosome, but power to localize beyond the chromosomal level
may be significantly compromised.[27] A full understanding of the
contribution of different susceptibility factors from this region will be
necessary as we seek to understand the genetic complexity of this
disease.
C Helms1 L Cao1 JG Krueger2 EM Wijsman3 F Chamian2 D
Gordon4 M Heffernan5 JA Wright-Daw1 J Robarge1 J Ott4 P-Y
Kwok6 A Menter7 AM Bowcock1
1Department of Genetics Washington University School of
Medicine St. Louis Missouri, 63110, USA.
2Laboratory for Investigative Dermatology The Rockefeller
University New York NY 10021, USA.
3Div. of Medical Genetics and Dept. Biostatistics University of
Washington Seattle Washington, 98195, USA.
4Lab of Statistical Genetics The Rockefeller University New York
NY 10021, USA.
5Div. Of Dermatology Washington University School of Medicine St. Louis Missouri, 6310, USA.
6Department of Dermatology Cardiovascular Research Institute,
and Center for Human Genetics University of California San
Francisco CA 94143, USA.
7Department of Internal Medicine Division of Dermatology Baylor
University Medical Center Dallas Texas, 75246 USA.
*Correspondence should be addressed to A.M.B. (email:
bowcock@genetics.wustl.edu).
References
1. Stuart P, Nair RP, Abecasis GR, Nistor I, Hiremagalore R, Chia
NV, Qin ZS, Thompson RA, Jenisch S, Weichenthal M, Janiga J,
Lim HW, Christophers E, Voorhees JJ, Elder JT. Analysis of
RUNX1 binding site and RAPTOR polymorphisms in psoriasis: No
evidence for Association Despite Adequate power and Evidence
for linkage. J Med Genet 2005 (online publication).
2. Tomfohrde J, Silverman A, Barnes R, Fernandez-Vina MA,
Young M, Lory D, Morris L, Wuepper KD, Stastny P, Menter, A.
Gene for familial psoriasis susceptibility mapped to the distal end
of human chromosome 17q. Science 1994;264:1141-5.
3. Helms C, Cao L, Krueger JG, Wijsman EM, Chamian F, Gordon
D, Heffernan M, Daw J, Robarge J, Ott J, Kwok P-Y, Menter A,
Bowcock AM. A putative RUNX1 binding site variant between
SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis.
Nat Genet 2003;35:349-56.
4. Sillanpaa MJ, Auranen K. Replication in genetic studies of
complex traits. Ann Hum Genet 2004;68:646-57.
5. Bross I. Misclassification in 2 x 2 tables. Biometrics
1954;10:478-86.
6. Mote VL, Anderson RL. An investigation of the effect of
misclassification on the properties of chisquare-tests in the
analysis of categorical data. Biometrika 1965;52:95-109.
7. Cochran WG. Errors of measurement in statistics. Technometrics
1968;10:637-666.
8. Ott J. Analysis of human genetic linkage: Johns Hopkins,
Baltimore, 1999.
9. Gordon D, Matise TC, Heath SC, Ott J. Power loss for multiallelic
transmission/disequilibrium test when errors introduced: GAW11
simulated data. Genet Epidemiol Suppl 1999;17:S587-S92.
10. Gordon D, Heath SC, Liu X, Ott J. A transmission/
disequilibrium test that allows for genotyping errors in the analysis
of single-nucleotide polymorphism data. Am J Hum Genet
2001;69:371-80.
11. Gordon D, Finch SJ, Nothnagel M, Ott J. Power and sample
size calculations for case-control genetic association tests when
errors are present: application to single nucleotide polymorphisms.
Hum Hered 2002;54:22-33.
12. Gordon D, Haynes C, Johnnidis C, Patel SB, Bowcock AM, Ott
J. A transmission disequilibrium test for general pedigrees that is
robust to the presence of random genotyping errors and any
number of untyped parents. Eur J Hum Genet 2004;12:752-61.
13. Zou G, Zhao H. The impacts of errors in individual genotyping
and DNA pooling on association studies. Genet Epidemiol
2004;26:1-10.
14. Zheng G, Tian X. The impact of diagnostic error on testing
genetic association in case-control studies. Stat Med 2005;24:869-
82.
15. Edwards BJ, Haynes C, Levenstien MA, Finch SJ, Gordon D.
Power and sample size calculations in the presence of phenotype
errors for case/control genetic association studies. BMC Genet
2005;6:18.
16. Suarez BK, Hampe CL, van Eerdewegh P. Problems of
replicating linkage claims in psychiatry. Washington: American
Psychiatric Press, 1994.
17 Goring HHH, Terwilliger JD, Blangero J (2001) Large upward
bias in estimation of locus-specific effects from genomewide scans
Am J Hum Genet 69:1357-1369.
18. Niu T. Algorithms for inferring haplotypes. Genet Epidemiol
2004;27:334-347.
19. Lindholm E, Zhang J, Hodge SE, Greenberg DA. The reliability
of haplotyping inference in nuclear families: misassignment rates
for SNPs and microsatellites. Hum Hered 2004;57:117-127.
20. Benjamini Y, Yekutieli D. Quantitative Trait Loci Analysis using
the False Discovery Rate. Genetics 2005.
21. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. Controlling
the false discovery rate in behavior genetics research. Behav
Brain Res 2001;125:279-84.
22. Perneger TV. Adjusting for multiple testing in studies is less
important than other concerns. BMJ 1999;318:1288.
24. Morel L, Blenman KR, Croker BP, Wakeland EK. The major
murine systemic lupus erythematosus susceptibility locus, Sle1, is
a cluster of functionally related genes. Proc Natl Acad Sci, USA
2001;98:1787-92.
25. Adeniji OA, Mrug MM, DiPalma JA. Not one but two
inflammatory bowel disease susceptibility loci map to chromosome
16. Am J Gastroenterol 2002;97:2464-5.
26. Hwu WL, Yang CF, Fann CS, Chen CL, Tsai TF, Chien YH,
Chiang SC, Chen CH, Hung SI, Wu JY, Chen YT. Mapping of
psoriasis to 17q terminus. J Med Genet 2005;42:152-8.
27. Gordon, D., Hoh, J., Finch, S.J., Levenstien, M.A., Edington, J.,
Li, W., Majewski, J. and Ott, J. Two approaches for consolidating
results from genome scans of complex traits: selection methods
and scan statistics. Genet Epidemiol 2001;21 Suppl 1, S396-402.
In a recent article, Debniak et al. have reported data from a case-control study of breast cancer in Poland in which a modest association was observed between breast cancer incidence and the A148T polymorphism in the CDKN2A gene. They observed an odds ratio of 1.3 overall, and an odds ratio of 3.8 for patients diagnosed prior to age 30. The variant was present in 5.1% of cases, versus 3.5% of controls. Their co...
In a recent article, Debniak et al. have reported data from a case-control study of breast cancer in Poland in which a modest association was observed between breast cancer incidence and the A148T polymorphism in the CDKN2A gene. They observed an odds ratio of 1.3 overall, and an odds ratio of 3.8 for patients diagnosed prior to age 30. The variant was present in 5.1% of cases, versus 3.5% of controls. Their control group was a mixture of newborns, and adults from the geographical region in which the cases
were obtained.
We have recently completed an international population-based study of melanoma in which mutation testing of the CDKN2A gene was performed. Our data consist of 3546 probands who were incident cases of melanoma, either a first or a subsequent primary. The frequency of the A148T variant was
observed to be 6.7% (237/3546), slightly higher than the frequency in the cases in the Debniak et al. study. The frequencies were 5.7% (79/1377) in Australian probands, 7.2% (145/1858) in North American probands, and 7.8% (13/166) in Italian probands, although these differences are not
statistically significant. In our study patients reported the occurrences of cancer in first degree relatives. Overall 18 breast cancers were reported among the 760 female relatives of probands with the A148T variant (2.4%) versus 320 (3.0%) among the 10809 female first degree relatives of
the non-carriers.
These data show no indication for an association of this variant with breast cancer in family members of melanoma probands, even after adjusting for age and geographic region. The data also show no evidence of an increased risk in younger family members.
We have read with great interest the excellent review entitled: "Genetics of familial intrahepatic cholestasis syndromes" by van Mil S. W. C. and collaborators, and published in the last issue of Journal of Medical Genetics. [1] In an attempt to complete this very exhaustive
review, we wished to make a few comments:
- concerning delta4-3-Oxosteroid-5beta reductase (AKR1D1) deficiency, since t...
We have read with great interest the excellent review entitled: "Genetics of familial intrahepatic cholestasis syndromes" by van Mil S. W. C. and collaborators, and published in the last issue of Journal of Medical Genetics. [1] In an attempt to complete this very exhaustive
review, we wished to make a few comments:
- concerning delta4-3-Oxosteroid-5beta reductase (AKR1D1) deficiency, since the human gene (AKR1D1, also named SRD5B1) was cloned, two recent publications [2,3] report 5 SRD5B1 mutations responsible for delta4-3-
Oxosteroid-5beta reductase deficiency in 5 patients. These data confirm that the disease is transmitted in a recessive autosomal pattern, and show that when delta4-3-Oxosteroid-5beta reductase deficiency is suspected on the basis of mass spectrometry analysis of urinary bile acids, diagnosis can be confirmed by molecular biology technology. This new diagnostic tool is important because patients with other severe liver diseases may present
an abnormal concentration of bile acids with 3-oxo-delta4 nuclear structure secondary to liver failure and not due to genetically determined enzyme defect.[4] So far it is admitted that only patients with a primary genetic defect may benefit from early primary bile acid therapy in order
to try to correct liver failure and to avoid liver transplantation.[2,3]
- concerning HSD3B7 deficiency, in our experience the patients never exhibit pruritus at presentation and during the disease course. Iatrogenic pruritus may occur under cholic acid therapy in case of accidental overdose. We therefore believe that absence of pruritus in presence of
cholestasis features is a strong sign indicating a possible primary bile acid synthesis defect.[5,6] Since the first report in 2000 of a patient harbouring homozygous HSD3B7 mutation, additional mutations have been identified in 15 patients.[6]
We hope these additional informations will favourably complete this excellent review.
Emmanuel Gonzales, M. D.
Emmanuel Jacquemin, M. D., Ph. D.
Pediatric Hepatology, Bicêtre Hospital, AP-HP, University of Paris XI,
Paris , France
References
van Mil SW, Houwen RH, Klomp LW. Genetics of familial
intrahepatic cholestasis syndromes.
J Med Genet 2005;42(6):449-63.
Lemonde HA, Custard EJ, Bouquet J, Duran M, Overmars H, Scambler PJ, Clayton PT. Mutations in SRD5B1 (AKR1D1), the gene encoding delta(4)-3-oxosteroid 5beta-reductase, in hepatitis and liver failure in infancy.
Gut 2003;52(10):1494-9
Gonzales E, Cresteil D, Baussan C, Dabadie A, Gerhardt MF, Jacquemin E. SRD5B1 (AKR1D1) gene analysis in delta(4)-3-oxosteroid 5beta-reductase deficiency: evidence for primary genetic defect. J Hepatol 2004;40(4):716-8.
Clayton PT, Patel E, Lawson AM, Carruthers RA, Tanner MS,
Strandvik B et al. 3-oxo-delta4 bile acids in liver disease. Lancet
1988;1:1283-4.
Jacquemin E, Setchell KDR, O’Connell NC, Estrada A, Maggiore G,
Schmitz J, Hadchouel M, Bernard O. A new cause of progressive intrahepatic
cholestasis: 3beta-hydroxy-C27-steroid dehydrogenase/isomerase deficiency.
J Pediatr 1994;125:379-84.
Cheng JB, Jacquemin E, Gerhardt M, Nazer H, Cresteil D, Heubi JE,
Setchell KDR, Russell DW. Molecular genetics of 3beta-hydroxy-delta5-C27-
steroid oxidoreductase deficiency in 16 patients with loss of bile acid
synthesis and liver disease. J Clin Endocrinol Metab 2003;88:1833-41.
We read with interest the paper of Kaiser-Rogers et al. [1] in which
they describe two cases of androgenetic/biparental mosaicism. In
their study both cases exhibited the clinicopathological phenotype
of placental mesenchymal dysplasia (PMD) and in both cases the
androgenetic cells were almost exclusively restricted to the
mesenchymal components of the villi, the overlying trophoblast
apparently bein...
We read with interest the paper of Kaiser-Rogers et al. [1] in which
they describe two cases of androgenetic/biparental mosaicism. In
their study both cases exhibited the clinicopathological phenotype
of placental mesenchymal dysplasia (PMD) and in both cases the
androgenetic cells were almost exclusively restricted to the
mesenchymal components of the villi, the overlying trophoblast
apparently being derived from normal biparental cells. In these
respects the cases in their report differ from those of a previous
case of androgenetic/biparental mosaicism described by us [2]
and cited by Kaiser-Rogers et al. [1]
We previously reported a case
of androgenetic / biparental mosaicism resulting in the live birth of a
phenotypically normal girl that, like the present cases, involved
only a single sperm. However, in the case described by us, the
trophoblast was composed of normal biparental cells in only some
villi, the trophoblast of other villi being exclusively androgenetic. In
our case the mesenchymal cells within the villus cores had the
same genotype as the overlying trophoblast in all areas examined,
unlike the present cases in which the mesenchyme and
trophoblast from the same villi appear to be genetically different.
Interestingly our case did not show any pathological evidence of
PMD but the androgenetic villi showed clear evidence of complete
hydatidiform mole phenotype with the biparental villi appearing
morphologically normal. The present study [1] suggests that
androgenetic/biparental mosaicism may be a cause of PMD but it
is clear that it may also have other phenotypic manifestations
according to the distribution of the androgenetic cells within the
placenta.
In our case the female child, now aged four, has
continued to develop normally suggesting that the androgentic
lineage was entirely confined to placental tissue or, if present, has
no pathological effects. Investigation of these rare cases by
molecular techniques may lead to greater understanding of both
normal placental development and the pathogenesis of these
unusual placental disorders.
Wilkinson et al. reported a Bedouin family in which five out of twelve
siblings had a complicated form of autosomal recessive spastic paraplegia. They
presented a uniform picture of early onset hereditary spastic paraplegia (HSP)
that began at 6-11 years of age with dysarthria, distal wasting of the upper
(UL) an...
Wilkinson et al. reported a Bedouin family in which five out of twelve
siblings had a complicated form of autosomal recessive spastic paraplegia. They
presented a uniform picture of early onset hereditary spastic paraplegia (HSP)
that began at 6-11 years of age with dysarthria, distal wasting of the upper
(UL) and lower limb (LL) muscles and emotional lability. Three affected
patients also had intellectual impairment, although it could not be determined
whether this resulted from mental retardation or cognitive decline. After
exclusion of linkage to the known autosomal recessive HSP loci, a genome-wide
scan identified a 22.8 cM region of homozygozity at 12p11.1-12q14 with a
maximum lod score of 5.1 that segregated in all affected individuals. This was
the first family linked to the locus designated SPG26.
We report here a new family of Spanish origin (family 112) with a
complicated form of autosomal recessive HSP linked to the same locus, that
extends the SPG26 phenotype and
refines the critical interval on chromosome 12. The parents, who were first
cousins, had four children, three of whom were affected. The clinical features
are summarized in table 1. Like the family reported by Wilkinson, our patients
presented a uniform clinical picture of early onset HSP that began at 8 to 10
years of age, dysarthria, distal UL and LL muscle wasting and mental
retardation. In addition, our patients also presented posterior capsule
cataracts at birth, peripheral axonal neuropathy, pes cavuswith
equinovarus and cerebellar
signs including axial instability, limb dysmetria, dysarthria, and horizontal
nystagmus. Some patients also had diplopia and altered vestibulo-ocular
reflexes.
The posterior capsule cataracts were assessed by an ophthalmologist.
Peripheral neuropathy was confirmed in patients 09 and 10 by electromyography and
measurement of nerve conduction velocities. Sensory action potentials were
absent in the LL and were greatly reduced in the UL. Sensory and motor nerve
conduction velocities were normal. The disability was severe. Patients 10 and
12 were wheelchair-bound at age 54 and 30, respectively, and patient 09 needed
two canes to walk at age 45. The father had an unremarkable examination at age
90. The mother, a year before she died at 88, had increased reflexes in the LL
and bilateral extensor plantar reflexes, in the absence of gait abnormality,
cataracts or mental retardation. She was therefore considered unaffected. The
unaffected sister had normal clinical examination at age 54.
Intellectual impairment in our patients was noted early and was not
progressive, suggesting mental retardation rather than cognitive deterioration.
The intellectual status of patient 09 was evaluated at age 45. He had a low IQ
(72), left school at age 20 and worked in a centre for the disabled. Patient 12
never went to school because of learning difficulties. In patients 09 and 10,
brain magnetic resonance imaging (MRI) showed cortical atrophy that was unusual
for their age (45 and 52). The cerebellum was normal.
After excluding
mutations in the coding exons of the SPG7
gene and linkage to known autosomal recessive HSP loci, we performed a
genome-wide scan with 400 microsatellite markers spaced approximately every
10cM using standard procedures. Positive multipoint lod score values (Z>1),
calculated with the ALLEGRO software (DECODE Genetics), were obtained for only
3 chromosomal regions. Twenty-eight additional markers were used to explore
these regions, two of which were excluded on the basis of haplotype
reconstruction and lod score values below the threshold of –2 (data not shown).
A maximal multipoint lod score of 2.53 was reached, however, in a 30cM region
flanked by markers D12S1617 and D12S1702. The minimal region of
homozygosity shared by the affected patients was defined by two recombination
events that occurred between markers D12S1617
and D12S345 in patient 12 and between
D12S1585 and D12S1686 in the unaffected sib (individual 11). This region
overlapped with the SPG26 candidate
interval, reducing it from 23 to 20 cM (figure not shown).
In conclusion,
this second family putatively linked to SPG26
extends the clinical phenotype of this complex form of HSP and refines the
critical region. There are more than 200 identified genes in this interval.
More families are therefore needed to further refine the locus and identify the
responsible gene.
Acknowledgments:
The authors are grateful to Drs Sylvie
Forlani and Merle Ruberg for their help as well as the DNA and cell Bank of
IFR-70 and the Centre National de Genotypage (Evry) for their help. PR was
supported by a fellowship from the European Neurological Society and the
Collège de Médecine des Hôpitaux de Paris. This work was funded by the Verum
Foundation (to AB) and the GIS-Rare Diseases Institute (to AD and GS).
1INSERM U679 (former U289) Federative Institute
for Neuroscience Research (IFR70), Salpêtrière Hospital, Paris, France; 2Department
of Genetics Cytogenetics and Embryology, AP-HP, Salpêtrière Hospital, Paris,
France, 3Federation of Neurology, AP-HP, Salpêtrière Hospital,
Paris, France, 4Salpêtrière Medical School, Pierre and Marie Curie
University, Paris, France, 5Department of Neurology and
Neuromuscular Diseases, La Timone Hospital, Marseille, France.
Address correspondence to Pr Alexis Brice, INSERM U679 (former U289),
Hôpital de la Salpêtrière, 47 Bd de l’Hôpital, 75013 Paris, France. E-mail: brice{at}ccr.jussieu.fr
References 1. Wilkinson PA, Simpson
MA, Bastaki L et al. A new locus for autosomal recessive
complicated hereditary spastic paraplegia (SPG26) maps to chromosome
12p11.1-12q14. J Med Genet (2005),42:80-2.
Table 1. Clinical features of the three
members of family 112 with a complicated form of AR-HSP linked to the SPG26 locus.
Sphincter disturbances, abolished myotatic reflexes
in the LL, diplopia
+: Presence of the corresponding sign,
-: Absence of the corresponding sign, NA: Not available, UL: Upper limbs, LL:
Lower limbs, VOR: Vestibulo-ocular reflex.
We read with great interest the paper of Cardinal and colleagues reporting findings of an Australian diagnostic MEN1 genetic testing service.1 Molecular genetic diagnosis of MEN1 has been possible since the identification of the MEN1 gene in 1997.2 In 2001, consensus guidelines outlining clinical criteria for MEN1 mutation testing were published.3 The gu...
We read with great interest the paper of Cardinal and colleagues reporting findings of an Australian diagnostic MEN1 genetic testing service.1 Molecular genetic diagnosis of MEN1 has been possible since the identification of the MEN1 gene in 1997.2 In 2001, consensus guidelines outlining clinical criteria for MEN1 mutation testing were published.3 The guidelines recommend genetic testing in a patient meeting clinical criteria for sporadic MEN1 (the presence of at least 2 out of 3 main MEN1-related tumours, i.e. parathyroid, pancreatic and pituitary) or familial MEN1 (as in sporadic MEN1 plus at least one first-degree relative with one or more main MEN1-related tumours), and in a patient suspicious of MEN1 (multiple parathyroid tumours before age 30, recurrent hyperparathyroidism, gastrinoma or multiple islet cell tumours at any age, and familial isolated hyperparathyroidism). These clinical criteria were defined on the basis of initial research findings, and therefore reports of how the criteria apply in routine clinical practice are important. Similar to the study of Cardinal and colleagues, we have also recently reported a large cohort of patients from the UK, who underwent MEN1 genetic testing at our diagnostic molecular genetics laboratory.4 Likewise, Klein and colleagues have analysed a large diagnostic laboratory series from the USA.5
The MEN1 mutation detection rates in the three diagnostic series are very similar with an overall mutation detection rate of 34%
(Table 1). In patients with 2 or more main MEN1-related tumours (i.e., fulfilling clinical criteria for MEN1), the pick up rates were 26% and 68% for sporadic and familial cases, respectively
(Table 1). These compare to the pick up rates in research cohorts of 52% in sporadic MEN1 and 87% in familial MEN1.4 These findings from the diagnostic laboratory series firmly support the guideline recommendation of MEN1 genetic testing in patients fulfilling the clinical criteria of sporadic or familial MEN1. These series also show that the likelihood of finding a MEN1 mutation increases in the presence of a family history, and also depends upon the clinical features. Patients with 3 main MEN1-related tumours (as compared to those with 2 tumours)4 and patients with a combination of parathyroid & pancreatic tumours (as compared to those with parathyroid and pituitary tumours)4,5 are more likely to yield a positive mutation result.
Whilst the importance of genetic testing in patients fulfilling clinical criteria for sporadic or familial MEN1 is generally accepted, it remains uncertain as to which of the patients with isolated MEN1-related tumours should be screened for an MEN1 mutation. Sporadic isolated MEN1-related tumours (such as parathyroid and pituitary) are fairly common in the general population, and it is not feasible to perform expensive and laborious MEN1 genetic testing in all such cases. Although we did not find MEN1 mutations in the 10 patients with sporadic hyperparathyroidism in our series, Cardinal and colleagues found a MEN1 mutation in one (out of 11) patient with sporadic hyperparathyroidism, suggesting that MEN1 genetic testing should be carried out in patients with early onset, multiglandular parathyroid tumours. Clearly, further studies with much larger cohorts of patients are necessary to establish clinical criteria for MEN1 genetic testing in patients with various sporadic isolated MEN1-related tumours or rarer combinations of different MEN1-related tumours. In many countries molecular genetic testing for MEN1 is carried out by a single national laboratory or a small number of nominated regional centres. This should allow the collection of clinical information from large cohorts of patients undergoing MEN1 mutation analysis, which is likely to facilitate the further definition of clinical criteria for MEN1 genetic testing.
B Vaidya1, AT Hattersley1 & S Ellard2
Departments of 1Endocrinology and 2Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Peninsula Medical School, Exeter, UK
References:
1. Cardinal JW, Bergman L, Hayward N, Sweet A, Warner J, Marks L, Learoyd D, Dwight T, Robinson B, Epstein M, Smith M, Teh BT, Cameron DP, Prins JB. A report of a national mutation testing service for the MEN1 gene: clinical resentations and implications for mutation testing. J Med Genet 2005;42:69-74.
2. Chandrasekharappa SC, Guru SC, Manickam P, Olufemi SE, Collins FS, Emmert-Buck MR, Debelenko LV, Zhuang Z, Lubensky IA, Liotta LA, Crabtree JS, Wang Y, Roe BA, Weisemann J, Boguski MS, Agarwal SK, Kester MB, Kim YS, Heppner C, Dong Q, Spiegel AM, Burns AL, Marx SJ. Positional cloning of the gene for multiple endocrine neoplasia-type 1. Science 1997;276:404-7.
3. Brandi ML, Gagel RF, Angeli A, Bilezikian JP, Beck-Peccoz P, Bordi C, Conte-Devolx B, Falchetti A, Gheri RG, Libroia A, Lips CJ, Lombardi G, Mannelli M, Pacini F, Ponder BA, Raue F, Skogseid B, Tamburrano G, Thakker RV, Thompson NW, Tomassetti P, Tonelli F, Wells SA, Marx SJ. Guidelines for diagnosis and therapy of MEN type 1 and type 2. J Clin Endocrinol Metab 2001;86:5658-71.
4. Ellard S, Hattersley AT, Brewer CM, Vaidya, B. Detection of an MEN1 gene mutation depends on clinical features and supports current referral criteria for diagnostic molecular genetic testing. Clin Endocrinol 2005; 62:169-175.
5. Klein RD, Salih S, Bessoni J, Bale AE. Clinical testing for multiple endocrine neoplasia type 1 in a DNA diagnostic laboratory. Genet Med 2005;7:131-8.
We read with interest the article by Cadet and colleagues in which
the authors propose “reverse cascade screening” by newborn screening for
HFE-related hereditary haemochromatosis as an efficient way of detecting
affected adults.[1]
Although HH is an ideal disease for which to undertake screening as
it is common and easy to prevent [2] and there should not be concerns of
insurance discrimina...
We read with interest the article by Cadet and colleagues in which
the authors propose “reverse cascade screening” by newborn screening for
HFE-related hereditary haemochromatosis as an efficient way of detecting
affected adults.[1]
Although HH is an ideal disease for which to undertake screening as
it is common and easy to prevent [2] and there should not be concerns of
insurance discrimination, [3] we believe it is unethical to offer population-
based screening of neonates.
There have been no definite cases of HFE-related haemochromatosis
causing organ damage reported in individuals prior to adulthood and
therefore knowledge of genetic risk is not useful to the individual until
adulthood.[4] There is anecdotal evidence of illness in children being
ascribed to haemochromatosis where it is clearly not the case.[4] Parents
may institute a low iron diet in the mistaken belief that this will
prevent disease in their offspring, a practice that can in fact be harmful
to the child. Finally, because the individual tested did not request the
testing, the information may be forgotten and never be passed on to the at-risk individual.
Since neonatal screening would not be of value to the individual for
at least 20 years and in fact could cause harm because of overzealous
dietary iron restriction or inappropriate phlebotomy, the idea of
screening a neonate to benefit his/her parents is a cause for even more
concern. Screening should be primarily for the benefit of that child, not
a third party.
A more appropriate time to offer screening for haemochromatosis may
be to high school students as we have shown in a school community in
Victoria, Australia.[5] The simple logistics of screening in a high school
enables informed consent since education programs can be easily delivered
in that setting. The individual at risk of haemochromatosis learns of
that result at a time that they can take appropriate steps to prevent iron
overload and thus disease morbidity.
Associate Professor Martin Delatycki
Dr Katie Allen
References
1. Cadet E, Capron D, Gallet M, et al. Reverse cascade screening of
newborns for hereditary haemochromatosis: a model for other late onset
diseases. J Med Genet 2005;42:390-395.
2. Delatycki M, Allen K, Nisselle A, et al. Use of community genetic
screening to prevent HFE-associated hereditary haemochromatosis. Lancet
2005; In Press.
3. Delatycki M, Allen K, Williamson R. Insurance agreement to facilitate
genetic testing. Lancet. 2002;359(9315):1433.
4. Delatycki MB, Powell LW, Allen KJ. Hereditary hemochromatosis genetic
testing of at-risk children: what is the appropriate age? Genet Test
2004;8(2):98-103.
5. Gason AA, Aitken MA, Metcalfe SA, et al. Genetic susceptibility
screening in schools: attitudes of the school community towards hereditary
haemochromatosis. Clin Genet 2005;67(2):166-74.
The conclusions of Rauch et al. [1] with respect to positive genotype-phenotype correlations in
22q11 Deletion Syndrome (22qDS) must be viewed with caution. They report on extensive
fluorescence in situ hybridization (FISH) studies of 350 patients with features of 22qDS ascertained
from 3 sources. Based on a case series of 3 subjects found to have distal (atypical) deletions that
would not have been detecte...
The conclusions of Rauch et al. [1] with respect to positive genotype-phenotype correlations in
22q11 Deletion Syndrome (22qDS) must be viewed with caution. They report on extensive
fluorescence in situ hybridization (FISH) studies of 350 patients with features of 22qDS ascertained
from 3 sources. Based on a case series of 3 subjects found to have distal (atypical) deletions that
would not have been detected using commonly used clinical probes (TUPLE1 or N25), they draw
provocative conclusions about genotype-phenotype associations. The methods used and data
presented do not justify the generalizations made, however.
We have calculated 95% confidence intervals (CIs) (see Table 1.) for the Rauch et al. data presented
since percentages alone may be misleading. CIs allow for an assessment of statistical significance
while accounting for sample size and rarity of events.[2] All of these CIs are non-significant, that
is contain expected values, such as ~18% for positive clinical FISH in conotruncal congenital heart
defect (ctCHD).[3] In addition, the 95% CI for finding three distal deletions in 350 subjects (0.86%)
is 0.18-2.5%, which overlaps the 0-5% frequency reported in the literature, as would the results if
only the sample of genetics referrals with features suggestive of 22qDS were used as the
denominator: 3/77 (3.9%, 95% CI 0.8-8.3%).
To support their assertion of a genotype-phenotype correlation, the authors compared the frequency of atypical distal deletions in a sub-sample (n=63) from the 77 genetics referrals to that in 3 other samples. However, using a selected partial sample prevents a proper interpretation of results, and limits applicability to other populations. If the 22qDS phenotype were the issue, the 77-subject
genetics referral sample should be used, since these subjects had multiple features consistent with
22qDS, as compared to those with a single feature such as ctCHD. On the other hand, if the issue
were whether "typical" 22qDS facial features were related to atypical distal deletions then the
relevant comparison should be between the 14 subjects with "typical" 22qDS facies and the 63
without these facies from the same ascertainment source. As illustrated in Table 2, the frequency
of distal deletions is significantly different (p<_0.05 no="no" correction="correction" for="for" multiple="multiple" comparisons="comparisons" in="in" only="only" _3="_3" non-overlapping="non-overlapping" all="all" of="of" which="which" involve="involve" deletions="deletions" distal="distal" to="to" the="the" _3mb="_3mb" region.="region." conclusion="conclusion" one="one" can="can" draw="draw" from="from" these="these" results="results" is="is" that="that" a="a" _22q11.2="_22q11.2" deletion="deletion" more="more" likely="likely" be="be" found="found" subjects="subjects" with="with" than="than" feature="feature" _22qds.="_22qds." _="_" p="p"/>
The assessment of atypicality of phenotypic expression is challenging in the phenotypically diverse condition 22qDS. Terms such as "atypical" should be used with caution as phenotype will vary with age, completeness of assessment, assessors, and ascertainment.[4] Mild learning difficulties may not be noticeable until later childhood, and absence of psychosis could not be truly determined until well into adulthood (in contrast to Table 3. of Rauch et al. where infants are indicated to have no
psychosis). Hyperactivity is a common feature in children with 22qDS.[5] The sister from the
affected sibpair with two different length 22q11.2 deletions may thus be considered to have typical
neurobehavioural features of 22qDS.
Larger sample sizes and detailed consideration of phenotypic and statistical methodology will be
needed before one can conclude that there is “a significant correlation between deletion site and
phenotypic expression” in 22qDS.
Anne S. Bassett, MD, FRCPC1,2 Rosanna Weksberg, PhD, MD, FRCPC3, 4 Eva W.C. Chow, MD, MPH, FRCPC1,2
1Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario,
Canada
2Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
3Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, Ontario, Canada
4Department of Molecular & Medical Genetics, University of Toronto, Toronto, Ontario, Canada
Table 1. Frequencies from Rauch et al. with percentages and 95% CI
22q11.2 deletions
Number
Sample
%
95 % CI*
Number
Sample
%
95 % CI*
Lower
Bound
Upper
Bound
Lower
Bound
Upper
Bound
Phenotype:
Conotruncal congenital heart defect (ctCHD)
Phenotype:
Genetics referrals with various features
suggestive of 22qDS
Positive clinical FISH
37
200
18.5
13.4
24.6
11
77
14.3
7.4
24.1
3 Mb (common)
33
200
16.5
11.6
22.4
11
77
14.3
7.4
24.1
1.5 Mb (proximal nested)
3
200
1.5
0.3
4.3
0
77
0
0
3.8
Atypical with proximal
extension
1
200
0.5
0.01
2.8
0
77
0
0
3.8
Atypical distal nested
0
200
0
0
1.5
1
77
1.3
0.03
7
Atypical distal to 3 Mb region
0
200
0
0
1.5
2
77
2.6
0.3
9.1
Negative clinical FISH
73
73
100
96
100
Atypical distal nested
0
73
0
0
4
Atypical distal to 3 Mb region
0
73
0
0
4
Multiple congenital anomalies and/or mental
retardation without features of 22qDS
(MCA/MR)
Healthy controls
Positive clinical FISH
0
100
0
0
3
3 Mb (common)
0
100
0
0
3
1.5 Mb (proximal nested)
0
100
0
0
3
Atypical distal nested
0
250
0
0
1.2
0
285
0
0
1
Atypical distal to 3 Mb region
0
300
0
0
1
0
285
0
0
1
*Where the frequency is 0, the 95% CI is one-sided
Table 2. Comparisons of frequency of distal deletions in different samples from Rauch et al. using Fisher’s exact testing*
Distal nested deletion
Deletions distal to
the 3Mb region
Any distal deletion
Group vs Genetics
Referral Sample
Parameters
p-value
Parameters
p-value
Parameters
p-value
Retrospective ctCHD
0/73 vs 1/77
1
0/73 vs 2/77
0.5
0/73 vs 3/77
0.25
Prospective ctCHD
0/200 vs 1/77
0.28
0/200 vs 2/77
0.08
0/200 vs 3/77
0.02
All ctCHD
0/273 vs 1/77
0.22
0/273 vs 2/77
0.048
0/273 vs 3/77
0.01
MCA/MR sample with data
on distally nested deletion
0/250 vs 1/77
0.24
not applicable
not applicable
MCA/MR sample with data
on deletions distal to the 3Mb
region
not applicable
0/300 vs 2/77
0.041
not applicable
Healthy controls
0/285 vs 1/77
0.21
0/285 vs 2/77
0.045
0/285 vs 3/77
0.009
Within the Genetic
Referral Sample
Typical facies vs. non-typical
facies
0/14 vs 1/63
1
0/14 vs 2/63
1
0/14 vs 3/63
1
*Statistically significant results are bolded
References
1. Rauch A, Zink S, Zweier C, Thiel CT, Koch A, Rauch R, Lascorz J, Huffmeier U, Weyand M,
Singer H, Hofbeck M. Systematic assessment of atypical deletions reveals genotype-phenotype
correlation in 22q11.2. J Med Genet 2005.
2. Richardson WS, Wilson MC, Williams JWJ, Moyer VA, Naylor CD. Users' guides to the medical
literature: XXIV. How to use an article on the clinical manifestations of disease. J Am Med Assoc
2000;284:869-875.
3. Goldmuntz E, Clark BJ, Mitchell LE, Jawad AF, Cuneo BF, Reed L, McDonald-McGinn D,
Chien P, Feuer J, Zackai EH, Emanuel BS, Driscoll DA. Frequency of 22q11 deletions in patients
with conotruncal defects. J Am Coll Cardiol 1998;32:492-498.
4. Cohen E, Chow EWC, Weksberg R, Bassett AS. Phenotype of adults with the 22q11 Deletion
Syndrome: A review. Am J Med Genet 1999;86:359-365.
5. Feinstein C, Eliez S, Blasey C, Reiss AL. Psychiatric disorders and behavioral problems in
children with velocardiofacial syndrome: Usefulness as phenotypic indicators of schizophrenia risk.
Biol Psychiatry 2002;51:312-318.
Dear Editor,
We are studying the genetic basis of non-syndromic hearing loss in North Indian population and we performed the PCR-RFLP assay described by authors for the detection of W24X mutation in this article. The assay was carried out using the primers (1F and 1R) and the restriction enzyme Alu1, as described by the authors. However, we have observed a distinctly different RFLP pattern for this mutation as compared...
Dear Editor,
We read with interest the recent article in the J Med Genet by Tessier et al.[1] confirming our report[2] of association between type 1 diabetes and the 2´5´-oligoadenylate synthetase OAS1 antiviral gene. However, their conclusion differs from ours concerning which single nucleotide polymorphism (SNP) in OAS1 is most likely to produce the functional effect on diabetes predisposition – the exon 3 non-...
Dear Editor,
In the recently published report "Analysis of RUNX1 Binding Site and RAPTOR Polymorphisms in Psoriasis: No Evidence for Association Despite Adequate Power and Evidence for Linkage"[1] the authors report failure to see association of psoriasis susceptibility to a region of chromosome 17q25. This region was first identified with linkage analysis by our group[2], and we recently reported evidence for a...
In a recent article, Debniak et al. have reported data from a case-control study of breast cancer in Poland in which a modest association was observed between breast cancer incidence and the A148T polymorphism in the CDKN2A gene. They observed an odds ratio of 1.3 overall, and an odds ratio of 3.8 for patients diagnosed prior to age 30. The variant was present in 5.1% of cases, versus 3.5% of controls. Their co...
Dear Editor,
We have read with great interest the excellent review entitled: "Genetics of familial intrahepatic cholestasis syndromes" by van Mil S. W. C. and collaborators, and published in the last issue of Journal of Medical Genetics. [1] In an attempt to complete this very exhaustive review, we wished to make a few comments:
- concerning delta4-3-Oxosteroid-5beta reductase (AKR1D1) deficiency, since t...
Dear Editor,
We read with interest the paper of Kaiser-Rogers et al. [1] in which they describe two cases of androgenetic/biparental mosaicism. In their study both cases exhibited the clinicopathological phenotype of placental mesenchymal dysplasia (PMD) and in both cases the androgenetic cells were almost exclusively restricted to the mesenchymal components of the villi, the overlying trophoblast apparently bein...
Dear Editor,
Wilkinson et al. reported a Bedouin family in which five out of twelve siblings had a complicated form of autosomal recessive spastic paraplegia. They presented a uniform picture of early onset hereditary spastic paraplegia (HSP) that began at 6-11 years of age with dysarthria, distal wasting of the upper (UL) an...
Dear Editor,
We read with great interest the paper of Cardinal and colleagues reporting findings of an Australian diagnostic MEN1 genetic testing service.1 Molecular genetic diagnosis of MEN1 has been possible since the identification of the MEN1 gene in 1997.2 In 2001, consensus guidelines outlining clinical criteria for MEN1 mutation testing were published.3 The gu...
Dear Editor,
We read with interest the article by Cadet and colleagues in which the authors propose “reverse cascade screening” by newborn screening for HFE-related hereditary haemochromatosis as an efficient way of detecting affected adults.[1]
Although HH is an ideal disease for which to undertake screening as it is common and easy to prevent [2] and there should not be concerns of insurance discrimina...
Dear Editor,
The conclusions of Rauch et al. [1] with respect to positive genotype-phenotype correlations in 22q11 Deletion Syndrome (22qDS) must be viewed with caution. They report on extensive fluorescence in situ hybridization (FISH) studies of 350 patients with features of 22qDS ascertained from 3 sources. Based on a case series of 3 subjects found to have distal (atypical) deletions that would not have been detecte...
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