Computational protocol: Hypomyelinating disorders in China: The clinical and genetic heterogeneity in 119 patients

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Protocol publication

[…] Genomic DNA was extracted from peripheral venous blood leukocytes from both patients and their families[], and genetic analysis was performed for all. The genetic analysis methods were chosen based on clinical diagnosis. HEXA or HEXB sequencing was taken for patients with deficiency of β-galactosidase or hexosaminidase A or B. For patients with PMD, the copy number variation of PLP1 were detected by multiplex ligation probe amplification (MLPA) using a SALSA MLPA P022 or P071 kit (MRC-Holland, Amsterdam, NH, NL), following the manufacturer’s protocol. The pattern of X-chromosome inactivation (XCI) was evaluated in the female patients with PLP1 mutations and ratios higher than 80:20 were considered skewed [][]. PLP1 sequencing was used for patients with negative MLPA results and if no mutations were found, GJC2 sequencing was used. Since 2013, targeted enrichment-based next-generation sequencing with 104 genes related with leukoencephalopathies or whole-exome sequencing were adopted for patients without definite genetic findings[]. The novelty of the variations was examined using the dbSNP (https://www.ncbi.nlm.nih.gov/projects/SNP/), HGMD (http://www.hgmd.cf.ac.uk/), ExAC (http://exac.broadinstitute.org/), and 1000G (http://www.internationalgenome.org/) databases. To evaluate probably pathogenic variations, analysis of the amino acid sequence conversation, family segregation, and verification on 100 normal alleles were performed. In silico prediction including mutationtaster (http://www.mutationtaster.org), Polyphen-2 (http://genetics.bwh.harvard.edu/pph2/), SIFT (http://sift.jcvi.org/), or HSF (http://umd.be/HSF3/) were used. For patients without positive NGS results, chromosomal abnormality was screened using high-resolution G-banding chromosome analysis on PHA-stimulated circulating lymphocytes (SRL, inc). […]

Pipeline specifications

Software tools MutationTaster, PolyPhen, SIFT
Databases dbSNP HGMD
Application WES analysis
Organisms Homo sapiens
Diseases Demyelinating Diseases, Leukodystrophy, Metachromatic, Nervous System Diseases, Gangliosidosis, GM1, Gangliosidoses, GM2, Pelizaeus-Merzbacher Disease, Trichothiodystrophy Syndromes