Copy Number Variation Analysis with Next Generation Sequencing

Abstract

Copy Number Variation Analysis with Next Generation Sequencing Bülent Uyanık1 , Sezin Canbek2 1 Bezmialem Vakıf Üniversitesi Tıp Fakültesi Tıbbi Genetik ABD. 2 Sağlık Bilimleri Üniversitesi Ümraniye Eğitim ve Araştırma Hastanesi Tıbbi Genetik Bölümü Objective: Aim of this study is present our medical genetics patients which have CNV mutations detected with NGS. Materials-Methods: We used The Clinical Exome Solution V2 kit (Sophia Genetics SA, Saint-Sulpice, Switzerland) for exome enrichment, with all procedures carried out according to the manufacturer’s protocols. This capture-based target enrichment kit covers 4490 genes with known inherited diseases causing mutations. Paired-end sequencing was performed on a NextSeq 500 system (Illumina, San Diego, CA, USA) with a read length of 150 x 2, while the base calling and image analysis were conducted using Real-Time Analysis (integrated to the NextSeq 500 system; Illumina) software. The BCL (base calls) binary is converted into FASTQ utilizing the Illumina package bcl2fastq. All bioinformatic analyses were performed on a Sophia DDM™ platform (Sophia Genetics SA), which includes algorithms for alignment, calling single nucleotide polymorphisms (SNPs) and small insertions/deletions (Pepper™, Sophia Genetics SA patented algorithm),calling copy number variations (Muskat™, Sophia Genetics SA patented algorithm). Results: This study shows that the next generation DNA sequencing method (with Sophia DDM ™) can display SNV, additionally heterozygous and homozygous deletions and duplications from single exonic to chromosomal levels. Conclusion: CNV analysis with NGS is an invaluable contribution to clinical practice. Keywords: CNV, NGS