Computational protocol: Agammaglobulinaemia despite terminal B-cell differentiation in a patient with a novel LRBA mutation

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Protocol publication

[…] The Illumina paired-end genomic DNA sample preparation kit (PE-102-1001, Illumina, San Diego, CA, USA) was used for preparing the libraries including end repair, A-tailing and ligation of the Illumina adaptors. Each sample was prepared with an index using the Illumina multiplexing sample preparation oligonucleotide kit (PE-400-1001, Illumina) and then pooled in batches of six in equimolar amounts prior to exome enrichment. The Illumina TruSeq exome kit (FC-121-1008, Illumina) was used to capture the human exome for each sample pool. Each 6-plex exome enriched library was sequenced in two lanes of an Illumina HiSeq 2000 with version 2 chemistry as 100 bp paired-end reads.Sequence reads were mapped to the GRCh37 assembly of the reference human genome using the default parameters of the Burrows–Wheeler Aligner ( Untrimmed reads were aligned allowing a maximum of two sequence mismatches and reads with multiple mappings to the reference genome were discarded along with PCR duplicates. Sequence variants were identified with SAMtools ( and annotated using Annovar ( […]

Pipeline specifications

Software tools BWA, SAMtools, ANNOVAR
Application WES analysis
Organisms Homo sapiens