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Segmentum: a tool for copy number analysis of cancer genomes.

Abstract Somatic alterations, including loss of heterozygosity, can affect the expression of oncogenes and tumor suppressor genes. Whole genome sequencing enables detailed characterization of such aberrations. However, due to the limitations of current high throughput sequencing technologies, this task remains challenging. Hence, accurate and reliable detection of such events is crucial for the identification of cancer-related alterations.
PMID
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Authors

Mayor MeshTerms

DNA Copy Number Variations

Loss of Heterozygosity

Software

Keywords

Cancer

Loss of heterozygosity

Segmentation

Somatic copy number analysis

Whole-genome sequencing

Journal Title bmc bioinformatics
Publication Year Start




PMID- 28407731
OWN - NLM
STAT- MEDLINE
DA  - 20170414
DCOM- 20170418
LR  - 20170418
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 18
IP  - 1
DP  - 2017 Apr 13
TI  - Segmentum: a tool for copy number analysis of cancer genomes.
PG  - 215
LID - 10.1186/s12859-017-1626-8 [doi]
AB  - BACKGROUND: Somatic alterations, including loss of heterozygosity, can affect the
      expression of oncogenes and tumor suppressor genes. Whole genome sequencing
      enables detailed characterization of such aberrations. However, due to the
      limitations of current high throughput sequencing technologies, this task remains
      challenging. Hence, accurate and reliable detection of such events is crucial for
      the identification of cancer-related alterations. RESULTS: We introduce a new
      tool called Segmentum for determining somatic copy numbers using whole genome
      sequencing from paired tumor/normal samples. In our approach, read depth and
      B-allele fraction signals are smoothed, and double sliding windows are used to
      detect breakpoints, which makes our approach fast and straightforward. Because
      the breakpoint detection is performed simultaneously at different scales, it
      allows accurate detection as suggested by the evaluation results from simulated
      and real data. We applied Segmentum to paired tumor/normal whole genome
      sequencing samples from 38 patients with low-grade glioma from the TCGA dataset
      and were able to confirm the recurrence of copy-neutral loss of heterozygosity in
      chromosome 17p in low-grade astrocytoma characterized by IDH1/2 mutation and lack
      of 1p/19q co-deletion, which was previously reported using SNP array data.
      CONCLUSIONS: Segmentum is an accurate, user-friendly tool for somatic copy number
      analysis of tumor samples. We demonstrate that this tool is suitable for the
      analysis of large cohorts, such as the TCGA dataset.
FAU - Afyounian, Ebrahim
AU  - Afyounian E
AD  - Faculty of Medicine and Life Sciences and BioMediTech institute, University of
      Tampere, Tampere, Finland.
FAU - Annala, Matti
AU  - Annala M
AD  - Faculty of Medicine and Life Sciences and BioMediTech institute, University of
      Tampere, Tampere, Finland.
FAU - Nykter, Matti
AU  - Nykter M
AD  - Faculty of Medicine and Life Sciences and BioMediTech institute, University of
      Tampere, Tampere, Finland. [email protected]
LA  - eng
PT  - Journal Article
DEP - 20170413
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - EC 1.1.1.41 (Isocitrate Dehydrogenase)
RN  - EC 1.1.1.41 (isocitrate dehydrogenase 2, human)
RN  - EC 1.1.1.42. (IDH1 protein, human)
RN  - Chromosome 1, monosomy 1p
SB  - IM
MH  - Astrocytoma/*genetics/pathology
MH  - Chromosome Deletion
MH  - Chromosomes, Human, Pair 1
MH  - Chromosomes, Human, Pair 17
MH  - Computer Simulation
MH  - *DNA Copy Number Variations
MH  - Genome-Wide Association Study
MH  - Glioma/*genetics/pathology
MH  - High-Throughput Nucleotide Sequencing/methods
MH  - Humans
MH  - Isocitrate Dehydrogenase/genetics
MH  - *Loss of Heterozygosity
MH  - Polymorphism, Single Nucleotide
MH  - Sequence Analysis, DNA
MH  - *Software
PMC - PMC5390478
OTO - NOTNLM
OT  - Cancer
OT  - Loss of heterozygosity
OT  - Segmentation
OT  - Somatic copy number analysis
OT  - Whole-genome sequencing
EDAT- 2017/04/15 06:00
MHDA- 2017/04/19 06:00
CRDT- 2017/04/15 06:00
PHST- 2016/05/27 [received]
PHST- 2017/04/06 [accepted]
AID - 10.1186/s12859-017-1626-8 [doi]
AID - 10.1186/s12859-017-1626-8 [pii]
PST - epublish
SO  - BMC Bioinformatics. 2017 Apr 13;18(1):215. doi: 10.1186/s12859-017-1626-8.

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