Journal of (2012) 57, 403–404 & 2012 The Japan Society of Human Genetics All rights reserved 1434-5161/12 $32.00 www.nature.com/jhg

COMMENTARY

An abundance of population-specific monomorphic SNPs may or may not be meaningful: a commentary on differences in frequencies of familial hypercholesterolemia SNPs in the Malaysian population

Wanna Thongnoppakhun, Anunchai Assawamakin and Sissades Tongsima

Journal of Human Genetics (2012) 57, 403–404; doi:10.1038/jhg.2012.52; published online 31 May 2012

n previous issue of the Journal of Human evaluating 310 previously reported ADH- morphic SNPs (28 out of 137) were IGenetics,Alexet al.1 report the differences associated SNPs mainly on the three ADH- reported, when comparing with other in allele frequencies of familial hypercho- causing and a few genes involved in the reported non-paralogous genes, APOB (73 lesterolemia (FH) single- polymor- cholesterol metabolic pathways. These SNPs SNPs) and PCSK9 (36 SNPs). phisms (SNPs) in the Malaysian population. under interrogation comprised either causa- Theauthors,however,claimedthat23 As one of the most common inherited tive SNPs or merely linked to ADH SNPs monomorphic SNPs in Malaysians are truly disorders in , autosomal dominant (as a signpost), whereas multiple-nucleotide unique as these SNPs in other populations hypercholesterolemia (ADH) (MIM #143890) polymorphisms, as well as structural varia- published elsewhere were reported as poly- or its more common name, FH is caused tions, were excluded from this study. Further- morphic. For example, the authors reported predominantly by mutations in LDLR in more, the platform was a rs61318752, which is a SNP in LDLR,asa the majority of patients. Additionally, less custom-designed microarray in which the monomorphic. Considering that some Malay- strong but important associations were also designed probes were based on common sians are of Chinese descent, on the contrary, identified for ApoE and PCSK9.Either SNPs from three databases, namely BHF, this rs61318752 SNP was previously reported heterozygous or homozygous mutations in dbSNP and SNPedia. for Han Chinese with MAF of 11.4%. Even these genes undoubtedly led to hypercho- The data presented by the authors were though population-specific monomorphic sites lesterolemia ranging from mild-to-severe interesting, that is, in both subject groups could be explained by either low mutation rate phenotypes. However, these findings under- 44.1% (137/310) monomorphic (mono-alle- or positive natural selection, before making play several previous studies highlighting the lic) SNPs were found. Their report is very such a conclusion, it is imperative to thor- importance of SNPs as genetic modifying similar in terms of number on other genes in oughly consider the study populations, patient factors in ADH, which affect cholesterol regu- African Americans or European Americans3 recruitment, SNP selection criteria, reliability lation differently across populations (revie- and the Danish population4.However,the of genotyping methods applied and publicly wed in Fahed and Nemer2). high proportion of invariable SNPs observed available SNP databases used for comparison. The article by Alex et al. aimed to identify could be caused either by a rare The research population studied by Alex ADH variants in self-identified multiethnic presented in the Human or et al. was 251 Malaysians consisting of Malaysians including 140 clinically diagnosed possibly by genotyping errors, frequently Malay (61.8%), Indian (22.7%) and Chinese FH patients and 111 healthy controls by found in the SNP database.5 Recently, (15.5%). Such samples are of Southeast Asian 8.32% of biallelic coding SNPs in dbSNP ancestry in which the data could provide a were classified as artifacts, called ‘single better understanding of genetic factors influ- nucleotide differences’ (SNDs), which result encing ADH by the race than those reported W Thongnoppakhun is at the Department of Research from highly similar (paralogous) genes.6 with European ancestry (reviewed in Fahed and Development, Division of Molecular Genetics, 2 Faculty of Medicine Siriraj Hospital, Mahidol University, LDLR, which has several paralogs including and Nemer ). However, using larger samples Bangkok, Thailand and A Assawamakin is at the National VLDLR, LRP, LRP1B, LRP8 and LRP1 that are ethnically homogeneous would be Center for Genetic Engineering and (www.genecards.org), is the only paralogous more appropriate as the allele frequency (BIOTEC), Pathum Thani, Thailand and S Tongsima is reported in Alex et al’s study. Given that estimated from small groups of controls at the National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand. the paralogs of LDLR potentially introduce deviates more from the true frequency than E-mail: [email protected]. SNDs, but only small number of mono- those from the larger ones.7 Alex et al. Commentary 404

recruited the ADH patients on the basis of 0.1285–0.3552), contributing to ADH mole- 4 Gaustadnes, M., Ørntoft, T. F., Jensen, J. L. & Torring, the commonly used Dutch Lipid Clinic cular research. The authors should not pre- N. Validation of the use of DNA pools and primer 8 extension in association studies of sporadic colorectal Network criteria. The SNP selection criteria maturely draw the conclusion that these cancer for selection of candidate SNPs. Hum. Mutat. were comprehensive and also based on effects SNPs could be the targets of positive selection 27, 187–194 (2006). of SNPs to the disease information collected using Fst values.12 However, further studies 5 Mitchell, A. A., Zwick, M. E., Chakravarti, A. & Cutler, D. J. Discrepancies in dbSNP confirmation rates and allele and curated in SNPedia (http://www.SNPedia. of the disease in Malaysians and possibly frequency distributions from varying genotyping error com).Nonetheless,thevariantcausalityin other Southeast Asian populations could rates and patterns. 20, 1022–1032 (2004). the analysis can be frequently misclassified utilize these data to select informative 6 Musumeci, L., Arthur, J.W., Cheung, F. S., Hoque, A., by either inclusion of non-causal variants or variants for either disease-associated studies Lippman, S. & Reichardt, J. K. Single nucleotide exclusion of causal variants9. Genotyping or molecular screening for preventive differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies. Hum. results by Alex et al. were validated by direct medicine in the future. Mutat. 31, 67–73 (2010). sequencing of randomly selected samples. 7 Taioli, E., Pedotti, P. & Garte, S. Importance of allele The authors compared their results with ACKNOWLEDGEMENTS frequency estimates in epidemiological studies. Mutat. Res. 567, 63–70 (2004). multiple SNP databases including dbSNP, WT is supported by ‘Chalermphrakiat’ Grant, 8 Civeira, F. Guidelines for the diagnosis and HAPMAP, mutDB and BHF to assess the Faculty of Medicine Siriraj Hospital, Mahidol management of heterozygous familial hypercholester- University. ST is supported in part by the Thailand olaemia. Atherosclerosis 173, 55–68 (2004). uniqueness of the SNPs uncovered across 9 Liu, D. J. & Leal, S. M. A novel adaptive method for the 10 Research Fund Grant number RSA5480026. worldwide populations. It would be better analysis of next-generation sequencing data to detect if a recent database of Pan-Asian population, complex trait associations with rare variants due to 11 gene main effects and interactions. PLoS. Genet. 6, PanSNPdb , was also taken into account. e1001156 (2010). The presence of monomorphic SNPs was 1 Alex, L., Chahil, J. K., Lye, S. H., Bagali, P. & 10 Doron, S & Shweiki, D. SNP Uniqueness Problem: a rarely mentioned and analyzed in previous Ler, L. W. Differences in allele frequencies of auto- proof-of-principle in HapMap SNPs. Hum. Mutat. 32, somal dominant hypercholesterolemia SNPs in the 355–357 (2011). reports. This is possibly due to publication Malaysian population. J. Hum. Genet. 57, 358–362 11 Ngamphiw, C., Assawamakin, A., Xu, S., Shaw, P. J., bias; positive findings were published, (2012). Yang, J. O., Ghang, H. et al. PanSNPdb: the Pan-Asian whereas negative ones were ignored. Alex 2 Fahed, A. C. & Nemer, G. M. Familial hypercholesterole- SNP genotyping database. PLoS. One 6, e21451 mia: the lipids or the genes? Nutr. Metab. 8, 23 (2011). (2011). et al. presented the first evaluation of popu- 3 Carlson, C. S., Eberle, M. A, Rieder, M. J., Smith, J. D., 12 Gardner, M., Williamson, S., Casals, F., Bosch, E., lation differentiation in allele frequencies Kruglyak, L. & Nickerson, D. A. Additional SNPs and Navarro, A., Calafell, F. et al. Extreme individual linkage-disequilibrium analyses are necessary for marker FST values do not imply population-specific for ADH-associated variants in Malaysians whole-genome association studies in humans. Nat. selection in humans: the NRG1 example. Hum. Genet. (as indicated by high Fst levels of Genet. 33, 518–521 (2003). 121, 759–762 (2007).

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