Target Enrichment Sequencing Protocol

Fastq files from the sequencer were redirected to a custom pipeline for HaloPlex^™ Target Enrichment System on the DNA nexus platform and/or to Agilent Surecall software.
Briefly, reads were aligned to the human reference genome (GRCh37/hg19) (http://hgdownload.cse.ucsc.edu/) with Burrows-Wheeler Aligner (BWA) [28 (link)] and variants were called using at least 2 of the 3 following variant callers: Genome Analysis Toolkit (GATK) [29 (link)–31 ], Freebayes [32 ] (both within the DNA nexus platform), and Base Alignment Quality (BAQ) Single Nucleotide Polymorphism (SNP) caller (within SureCall tool).
Variants passing quality filters were annotated separately against NCBI RefGene (http://www.ncbi.nlm.nih.gov) and ENSEMBL Variant Effect Predictor ver.72 (http://www.ensembl.org/info/docs/tools/vep).

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Ortega-Moreno L., Giráldez B.G., Soto-Insuga V., Losada-Del Pozo R., Rodrigo-Moreno M., Alarcón-Morcillo C., Sánchez-Martín G., Díaz-Gómez E., Guerrero-López R, & Serratosa J.M. (2017). Molecular diagnosis of patients with epilepsy and developmental delay using a customized panel of epilepsy genes. PLoS ONE, 12(11), e0188978.

Publication 2017

HaloPlex™ Target Enrichment System Surecall software

Genome Genome human Nexus Single nucleotide polymorphism

Corresponding Organization : Centre for Biomedical Network Research on Rare Diseases

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Variable analysis

independent variables

Alignment of reads to the human reference genome (GRCh37/hg19)
Variant calling using at least 2 of the 3 variant callers: GATK, Freebayes, and BAQ SNP caller

dependent variables

Variants passing quality filters

control variables

Not explicitly mentioned

positive controls

Not mentioned

negative controls

Not mentioned

Annotations

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