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Pipeline publication

[…] a frequency of 0.000008239 representing one individual of South Asian descent in the ExAC database (), with no homozygotes present at this position. Confirmation of the single-nucleotide variant in both children and their parents was performed using polymerase chain reaction (PCR) and Sanger sequencing, which verified the mutation was inherited from the mother, who was also heterozygous (). The phenotypic presentation in the children corresponded to the description of BTBGD in the literature; however, no other candidate SNP or indels in SLC19A3 were identified., To investigate the SLC19A3 locus for structural variants, the WGS read alignments were visualized with Integrated Genomics Viewer (IGV, 2.3.55) (http://software.broadinstitute.org/software/igv; ) and inspected for regions of altered coverage and alignment of discordant read pairs. This identified a region of reduced coverage, bordered by discordant reads encompassing exon 1 encoding the 5′ untranslated region (5′ UTR) (). The candidate deletion was also detected by copy-number variant detection algorithms: CNVnator (based on alterations in read depth) and BreakDancer (based on paired-end information) (; ). The precise breakpoints were mapped by PCR and Sanger sequencing to GRCh37 Chr2:228,582,251–228,587,060 (NC_000002.11:g.228,582,251–228,587,060 del) with the insertion of a cytosine nucleotide (summarized in ). This 4808-bp deletion is present in both children and PCR analysis confirmed inheritance from the father. We hypothesize that this deletion abolishes the activity of the promoter, thus eliminating expression from this allele. RNA-seq analysis of RNA from fibroblasts of the surviving child, AM1006, and three unrelated controls did not detect any reads mapping to the SLC19A3 gene; in contrast SLC19A1 and SLC19A2 were well expressed in […]

Pipeline specifications

Software tools IGV, CNVnator, BreakDancer
Organisms Homo sapiens
Chemicals Azoles, Biotin, Pyrimidines, Azoles, Thiazoles