title: Targeted resequencing of 9p in acute lymphoblastic leukemia yields concordant results with array CGH and reveals novel genomic alterations.
abstract: Genetic alterations of the short arm of chromosome 9 are frequent in acute lymphoblastic leukemia. We performed targeted sequencing of 9p region in 35 adolescent and adult acute lymphoblastic leukemia patients and sought to investigate the sensitivity of detecting copy number alterations in comparison with array comparative genomic hybridization (aCGH), and besides, to detect novel genetic anomalies. We found a high concordance of copy number variations (CNVs) as detected by next generation sequencing (NGS) and aCGH. By both methodologies, the recurrent deletion at CDKN2A/B locus was identified, whereas NGS revealed additional, small regions of CNVs, seen more frequently in adult patients, while aCGH was better at detecting larger CNVs. Also, by NGS, we detected novel structural variations, novel SNVs and small insertion/deletion variants. Our results show that NGS, in addition to detecting mutations and other genetic aberrations, can be used to study CNVs.
authors: Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Finland.
authors: Virinder Kaur
authors: VK
authors: Sarhadi
authors: Leo
authors: L
authors: Lahti
authors: Ilari
authors: I
authors: Scheinin
authors: Anne
authors: A
authors: Tyybäkinoja
authors: Suvi
authors: S
authors: Savola
authors: Anu
authors: A
authors: Usvasalo
authors: Riikka
authors: R
authors: Räty
authors: Erkki
authors: E
authors: Elonen
authors: Pekka
authors: P
authors: Ellonen
authors: Ulla M
authors: UM
authors: Saarinen-Pihkala
authors: Sakari
authors: S
authors: Knuutila
mesh_terms: D000293:Adolescent; D000328:Adult; D002869:Chromosome Aberrations; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D005260:Female; D019942:Genes, p16; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*; D055815:Young Adult
keywords: 9p deletion; Chromosome 9; Copy number variations; Next generation sequencing; aCGH