Analysis of CTG repeat length variation in theDMPKgene in the general population and the molecular diagnosis of myotonic dystrophy type 1 in Malaysia

Abstract

ObjectiveThe lack of epidemiological data and molecular diagnostic services in Malaysia has hampered the setting-up of a comprehensive management plan for patients with myotonic dystrophy type 1 (DM1), leading to delayed diagnosis, treatment and support for patients and families. The aim of this study was to estimate the prevalence of DM1 in the 3 major ethnic groups in Malaysia and evaluate the feasibility of a single tube triplet-primed PCR (TP-PCR) method for diagnosis of DM1 in Malaysia.Design, setting and participantsWe used PCR to determine the size of CTG repeats in 377 individuals not known to be affected by DM and 11 DM1 suspected patients, recruited from a tertiary hospital in Kuala Lumpur. TP-PCR was performed on selected samples, followed by Southern blot hybridisation of PCR amplified fragments to confirm and estimate the size of CTG expansion.Outcome measuresThe number of individuals not known to be affected by DM with (CTG)>18 was determined according to ethnic group and as a whole population. The χ2 test was performed to compare the distribution of (CTG)>18 with 12 other populations. Additionally, the accuracy of TP-PCR in detecting CTG expansion in 11 patients with DM1 was determined by comparing the results with that from Southern blot hybridisation.ResultsOf the 754 chromosomes studied, (CTG)>18 frequency of 3.60%, 1.57% and 4.00% in the Malay, Chinese and Indian subpopulations, respectively, was detected, showing similarities to data from Thai, Taiwanese and Kuwaiti populations. We also successfully detected CTG expansions in 9 patients using the TP-PCR method followed by the estimation of CTG expansion size via Southern blot hybridisation.ConclusionsThe results show a low DM1 prevalence in Malaysia with the possibility of underdiagnosis and demonstrates the feasibility of using a clinical and TP-PCR-based approach for rapid and cost-effective DM1 diagnosis in developing countries.

A reference haplotype panel for genome-wide imputation of short tandem repeats

“…Frequencies for DM1 were obtained from Fig. 1 of Ambrose et al 35 and are based on 254 controls of Chinese origin. Frequencies for HDL were obtained from Fig.…”

A deep population reference panel of tandem repeat variation

“…Control allele frequencies for disease-associated TRs were obtained from various sources: (1) HTT: Validated repeat lengths were obtained from Huntington’s Disease patients (dbGaP accession phs000371.v2.p1). We used non-expanded alleles from table pht002988.v1.p1.c1 to estimate control allele frequencies in European samples, for other populations, allele frequencies were extracted from Masuda, et al 58 (EAS), Baine, et al (AFR and H3Africa) 59 , Saleem, et al 60 (SAS), and Paradisi, et al 61 (AMR); (2) DMPK: Allele frequencies were obtained from Ambrose, et al 62 (EAS), Acton, et al 63 (AFR), and Magana, et al 64 (AMR); (3) PPP2R2B: Allele frequencies for Europeans were obtained from Majounie, et al 65 .…”

A reference haplotype panel for genome-wide imputation of short tandem repeats

“…Multi-sample calling allows HipSTR to leverage information on haplotypes discovered across all samples in the dataset to estimate per-locus error parameters and output genotype likelihoods for each possible diploid genotype. Notably, our HipSTR catalog excluded most known STRs implicated in expansion disorders such as Huntington's Disease and hereditary ataxias, since even the normal allele range for these STRs is above or near the length of Illumina reads [32][33][34][35] . To supplement our panel, we additionally used Tredparse 36 to genotype a targeted set of known pathogenic STRs in our cohort ( Supplementary Table 1 ).…”

“…Allele frequencies for SCA1, SCA2, SCA3, SCA6, SCA12, SCA8, SCA17, and DRPLA were obtained from Figure 1 of Majounie, et al 32 and are based on 307 controls of Welsh origin. Frequencies for DM1 were obtained from Figure 1 of Ambrose, et al 33 and are based on 254 controls of Chinese origin. Frequencies for HDL were obtained from 34 and are based on 352 controls of North American Caucasian origin.…”