Computational protocol: Familial monophasic acute transverse myelitis due to the pathogenic variant in VPS37A

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Protocol publication

[…] We performed whole-exome sequencing (WES) in 2 affected sisters and their 2 healthy brothers and 1 healthy sister. We captured the consensus coding sequence exonic regions and flanking intronic regions totaling ∼51 Mb using the Agilent SureSelect XT kit and performed paired-end 100 bp reads with the Illumina HiSeq 2500 platform. We aligned each read to the 1000 Genomes phase 2 (GRCh37) human genome reference with the Burrows-Wheeler Alignment v.0.5.10-tpx. Local realignment around indels and base call quality score recalibration were performed using the Genome Analysis Toolkit (GATK) v.2.3-9-ge5ebf34. Variant filtering was performed by the Variant Quality Score Recalibration method. For single nucleotide variants (SNVs), the annotations of MQRankSum, HaplotypeScore, QualByDepth, FisherStrand, RMSMappingQuality, and ReadPosRankSum were used in the adaptive error model (6 maximum Gaussians allowed, worst 3% used for training the negative model). HapMap3.3 and Omni2.5 were used as training sites, with HapMap3.3 used as the truth set. SNVs were filtered to obtain all variants up to the 99th percentile of truth sites (1% false-negative rate). For indels, the annotations of QD, FS, HaplotypeScore, and ReadPosRankSum were used in the adaptive error model (4 maximum Gaussians allowed, worst 12% used for training the negative model; indels that had annotations more than 10 SD from the mean were excluded from the Gaussian mixture model). A set of curated indels obtained from the GATK resource bundle (Mills_and_1000 G_gold_standard.indels.b37.vcf) were used as training and truth sites. Indels were filtered to obtain all variants up to the 95th percentile of truth sites (5% false-negative rate).Using the PhenoDB Variant Analysis Tool of PhenoDB, we prioritized heterozygous, homozygous, and compound heterozygous rare functional variants (missense, nonsense, splice-site variants, and indels) shared by the proband and her affected sister but not present in the 2 healthy brothers and healthy sister. We excluded variants with a minor allele frequency of >0.01 in Single Nucleotide Polymorphism database 126, 129, and 131, the Exome Variant Server (release ESP6500SI-V2), 1000 Genomes Project, or among the samples sequenced at classless interdomain routing (CIDR) as part of the Baylor-Hopkins Center for Mendelian Genomics. We also excluded all variants found in our in-house controls (CIDRVar 51 Mb). We generated a list of heterozygous variants shared by the proband and her affected sister but not present in the 3 healthy brothers and sister; a list of homozygous variants shared by the proband and her affected sister but excluding variants that were homozygous in one of the healthy siblings and a list of compound heterozygous variants identified shared by the proband and her affected sister but excluding the genes that had the same set of variants in one of the unaffected siblings. […]

Pipeline specifications

Software tools GATK, VARIANT
Databases CCDS PhenoDB
Application WES analysis
Organisms Homo sapiens
Diseases Urinary Bladder Diseases, Brain Diseases, Multiple Sclerosis, Myelitis, Transverse, Neuromyelitis Optica