Limits...
Estimation of copy number alterations from exome sequencing data.

Valdés-Mas R, Bea S, Puente DA, López-Otín C, Puente XS - PLoS ONE (2012)

Bottom Line: Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv.We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays.Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain.

ABSTRACT
Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using data from 86 paired normal and primary tumor samples, we identified losses and gains of complete chromosomes or large genomic regions, as well as smaller regions affecting a minimum of one gene. Comparison with high-resolution comparative genomic hybridization (CGH) arrays revealed a high sensitivity and a low number of false positives in the copy number estimation between both approaches. We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays. Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.

Show MeSH

Related in: MedlinePlus

Comparison between CNAs detected by exome2cnv and aCGH.Grey dots represent log2 ratios of tumor/normal probe intensities from aCGH, while black dots show log2 ratios of tumor/normal from exome sequencing data. The local averages determined for exome data (red lines) and aCGH data (green lines) are shown. (a) Homozygous deletion of a small region of chromosome 13 detected by both approaches. (b) Detailed view of the same chromosomal region shown in (a).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3526607&req=5

pone-0051422-g004: Comparison between CNAs detected by exome2cnv and aCGH.Grey dots represent log2 ratios of tumor/normal probe intensities from aCGH, while black dots show log2 ratios of tumor/normal from exome sequencing data. The local averages determined for exome data (red lines) and aCGH data (green lines) are shown. (a) Homozygous deletion of a small region of chromosome 13 detected by both approaches. (b) Detailed view of the same chromosomal region shown in (a).

Mentions: By comparing exome data from the tumor sample with its matched non-tumor cells we were able to detect several somatic CNAs affecting autosomes which were also found using aCGH data (Figure 3 and Tables S1 and S2). They involved homozygous or heterozygous deletion of large chromosomal regions (in chromosomes 6, 11, 13, 17 or 20), gains of whole chromosomes (chromosome 12) or large chromosomal regions (in chromosomes 2, 3, and 4), as well as other smaller regions including deletion of the RFX7 gene or deletion of six exons of SLC9A9. In addition, we detected both homozygous and heterozygous deletions of a small fragment of chromosome 13q14 frequently deleted in CLL tumors [8], [38], [39] (Figure 3 and Figure 4) and resulting in the deletion of two microRNAs (miR15a and miR16-1) frequently lost in this pathology [38]. Trisomy of chromosome 12, a frequent alteration present in CLL tumors, was also identified using exome2cnv. Together, these results show that this procedure allows the identification of most types of CNAs that might be present in cancer samples, including heterozygous and homozygous deletions as well as amplified genomic regions.


Estimation of copy number alterations from exome sequencing data.

Valdés-Mas R, Bea S, Puente DA, López-Otín C, Puente XS - PLoS ONE (2012)

Comparison between CNAs detected by exome2cnv and aCGH.Grey dots represent log2 ratios of tumor/normal probe intensities from aCGH, while black dots show log2 ratios of tumor/normal from exome sequencing data. The local averages determined for exome data (red lines) and aCGH data (green lines) are shown. (a) Homozygous deletion of a small region of chromosome 13 detected by both approaches. (b) Detailed view of the same chromosomal region shown in (a).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3526607&req=5

pone-0051422-g004: Comparison between CNAs detected by exome2cnv and aCGH.Grey dots represent log2 ratios of tumor/normal probe intensities from aCGH, while black dots show log2 ratios of tumor/normal from exome sequencing data. The local averages determined for exome data (red lines) and aCGH data (green lines) are shown. (a) Homozygous deletion of a small region of chromosome 13 detected by both approaches. (b) Detailed view of the same chromosomal region shown in (a).
Mentions: By comparing exome data from the tumor sample with its matched non-tumor cells we were able to detect several somatic CNAs affecting autosomes which were also found using aCGH data (Figure 3 and Tables S1 and S2). They involved homozygous or heterozygous deletion of large chromosomal regions (in chromosomes 6, 11, 13, 17 or 20), gains of whole chromosomes (chromosome 12) or large chromosomal regions (in chromosomes 2, 3, and 4), as well as other smaller regions including deletion of the RFX7 gene or deletion of six exons of SLC9A9. In addition, we detected both homozygous and heterozygous deletions of a small fragment of chromosome 13q14 frequently deleted in CLL tumors [8], [38], [39] (Figure 3 and Figure 4) and resulting in the deletion of two microRNAs (miR15a and miR16-1) frequently lost in this pathology [38]. Trisomy of chromosome 12, a frequent alteration present in CLL tumors, was also identified using exome2cnv. Together, these results show that this procedure allows the identification of most types of CNAs that might be present in cancer samples, including heterozygous and homozygous deletions as well as amplified genomic regions.

Bottom Line: Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv.We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays.Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain.

ABSTRACT
Exome sequencing constitutes an important technology for the study of human hereditary diseases and cancer. However, the ability of this approach to identify copy number alterations in primary tumor samples has not been fully addressed. Here we show that somatic copy number alterations can be reliably estimated using exome sequencing data through a strategy that we have termed exome2cnv. Using data from 86 paired normal and primary tumor samples, we identified losses and gains of complete chromosomes or large genomic regions, as well as smaller regions affecting a minimum of one gene. Comparison with high-resolution comparative genomic hybridization (CGH) arrays revealed a high sensitivity and a low number of false positives in the copy number estimation between both approaches. We explore the main factors affecting sensitivity and false positives with real data, and provide a side by side comparison with CGH arrays. Together, these results underscore the utility of exome sequencing to study cancer samples by allowing not only the identification of substitutions and indels, but also the accurate estimation of copy number alterations.

Show MeSH
Related in: MedlinePlus