Computational protocol: Identification and functional analysis of a novel LHX1 mutation associated with congenital absence of the uterus and vagina

Similar protocols

Protocol publication

[…] We sequenced exomes of the ten unrelated CAUV patients. All exons were captured by NimbleGen Human All Exon Enrichment kit and then massively parallel sequenced on Illumina Hiseq 2500 platform. We used BWA v0.5.9 [] to align reads to reference human genome (GRC build 37), Picardtools to mark and remove duplicates, Samtools to detect SNPs and indels, and ANNOVAR [] to annotate all variants. We only focused on functional variants (missense, nonsense, splicing site and frame-shift) with a minor allele frequency (MAF) less than 1% in public and in House databases. Frequency-filtered variants were then predicted in silico to assess their impact on the function and structure of encoded proteins. The analysis process referred to the article we published before []. The candidate gene detected by whole-exome sequencing was validated by Sanger sequencing. […]

Pipeline specifications

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