FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY: CLINICAL AND GENETIC DIAGNOSIS
CitationLi, Kun. 2022. FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY: CLINICAL AND GENETIC DIAGNOSIS. Master's thesis, Harvard Medical School.
AbstractBackground: Facioscapulohumeral muscular myodystrophy (FSHD) is a hereditary myodystrophy typically affecting skeletal muscles of the facial muscles, shoulder girdles, and upper arms. The clinical course of FSHD is highly variable and the heart is rarely involved. We aim to describe the detailed clinical characteristics of an unusual FSHD case. The existing FSHD1 diagnostic approaches, including Southern blot and Molecular combing, are not widely used for the reason of time-consuming, labor-intensive, and high equipment requirements. We aim to develop an efficient and accurate procedure for the diagnosis of FSHD.
Methods: We collected data for the family members. Whole genome sequencing was performed for ten individuals from a large FSHD family. Parametric linkage analysis was performed via Merlin (v1.1.2) with the following parameters: dominant model, an estimated population allele frequency of 1E-5, and penetrance of 90%. 4q and 10q haplotypes were characterized by alignment to the chm13 reference genome. A BLAT of the pLAM sequence were performed to identify the A/B haplotypes. We realigned the 250-bp paired end whole genome sequencing reads to the chm13 reference genome using BWA-MEM and then measured the read count for reads containing either the 4q-specific D4Z4 sequence of 4q-specific pLAM sequence and normalized counts to the read depth of the p-arm of chromosome 4.
Results: Rare variants-based linkage analysis identified one single 1.7 MB haplotype on chromosome 4q35.2, presenting in affected individuals and absent from unaffected family members. Parametric linkage analysis resulted in a LOD score of 3.228 for the region. All pedigree samples contained 4q-pLAM sequence suggesting at least one copy of an 4qA permissive haplotype. Normalized counts of reads containing 4q-specific pLAM sequence were comparable between the FSHD patients, while 4q-specific D4Z4 repeat sequence demonstrated fewer reads in pedigree samples.
Conclusion: Family WGS and rare variants-based linkage analyses, combined with read depth analysis, provide the possibility of detecting the D4Z4 repeat contraction for FSHD1 patients. 4q pLAM specific sequence could be detected by matching to T2T-CHM13 reference.
Citable link to this pagehttps://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37371578