Computational protocol: A Mild Form of SLC29A3 Disorder: A Frameshift Deletion Leads to the Paradoxical Translation of an Otherwise Noncoding mRNA Splice Variant

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Protocol publication

[…] We genotyped the two patients (P1 and P2) and their parents (I.1 and I.2) with the Affymetrix genome-wide SNP array 6.0 (Affymetrix, Santa Clara, CA) comprising 909,622 SNPs, at the Rockefeller University Genomics Resource Center. Genotyping was highly successful, with call rates of 98 to 99% across study subjects. Only autosomal chromosome SNPs with a 100% call rate and a minor allele frequency (MAF) >0.25 among parents were retained, and no Mendelian errors were allowed, leaving 342,565 high-quality SNPs for linkage analysis. Genome-wide homozygosity mapping was performed using MERLIN , under a recessive model, with penetrance set to 0.9 and no allowance for sporadic cases. Multipoint LOD scores were obtained at each position, and regions longer than 1 Mb in length attaining the maximum LOD score of 1.8 for the family were defined as priority regions for the screening of exome sequencing data. [...] Exome capture was performed with the Agilent SureSelect Human All Exon 38 Mb kit (Agilent Technologies). Single-end sequencing was performed on an Illumina Genome Analyzer IIx (Illumina) generating 72-base reads. We aligned the sequences with the hg19 reference build of the human genome, using the Burrows-Wheeler Aligner . Downstream processing and variant calling were carried out with the Genome Analysis Toolkit (GATK) , Samtools and Picard tools (http://picard.sourceforge.net). Substitution and indel calls were made with GATK Unified Genotyper. All calls with read coverage 4× and a phred-scaled SNP quality of 30 were filtered out. Variants were annotated with GATK GenomicAnnotator. […]

Pipeline specifications

Software tools Merlin, BWA, GATK, SAMtools, Picard
Application WES analysis
Organisms Homo sapiens
Diseases Dental Caries, Diabetes Mellitus, Type 1, Hypertrichosis, Rhinoscleroma, Histiocytosis, Sinus, Genetic Diseases, Inborn