Bivariate segmentation of SNP-array data for allele-specific copy number analysis in tumour samples

AbstractMotivationCopy number variations (CNVs) are gains and losses of DNA segments and have been associated with disease. Many large-scale genetic association studies are performing CNV analysis using whole exome sequencing (WES) and whole genome sequencing (WGS). In many of these studies, previous SNP-array data are available. An integrated cross-platform analysis is expected to improve resolution and accuracy, yet there is no tool for effectively combining data from sequencing and array platforms. The detection of CNVs using sequencing data alone can also be further improved by the utilization of allele-specific reads.ResultsWe propose a statistical framework, integrated Copy Number Variation detection algorithm (iCNV), which can be applied to multiple study designs: WES only, WGS only, SNP array only, or any combination of SNP and sequencing data. iCNV applies platform specific normalization, utilizes allele specific reads from sequencing and integrates matched NGS and SNP-array data by a Hidden Markov Model (HMM). We compare integrated two-platform CNV detection using iCNV to naive intersection or union of platforms and show that iCNV increases sensitivity and robustness. We also assess the accuracy of iCNV on WGS data only, and show that the utilization of allele-specific reads improve CNV detection accuracy compared to existing methods.Availabilityhttps://github.com/zhouzilu/[email protected], [email protected] informationSupplementary data are available at Bioinformatics online.

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Uniparental Disomy May Be Associated with NPM Mutations in AML with a Normal Karyotype.

Blood ◽

10.1182/blood.v108.11.2310.2310 ◽

2006 ◽

Vol 108 (11) ◽

pp. 2310-2310

Author(s):

Elena Serrano ◽

Vanesa Orantes ◽

Camino Estivill ◽

Adriana Lasa ◽

Salut Brunet ◽

...

Keyword(s):

Complete Remission ◽

Copy Number ◽

Germ Line ◽

Snp Array ◽

Uniparental Disomy ◽

Normal Karyotype ◽

Copy Number Analysis ◽

Complex Germ ◽

Flt3 Mutations ◽

Tandem Duplications

Abstract Acute myeloid leukemia (AML) is a heterogeneous group of neoplastic disorders characterized by an abnormal proliferation of the myeloid precursors and a maturation block. A large proportion of AML cases have either a normal karyotype or non-recurrent chromosomal alterations. Underlying genetic lesions of some of these cases have been characterized with the discovery of MLL-internal tandem duplications, activating FLT3 mutations and NPM mutations. Loss of heterozygosity (LOH) derives from the loss of one of the two alleles at a given locus and can be a sign of inactivation of tumor-suppressor genes. We performed a high-resolution genotype analysis on DNA obtained from 19 AML patients with a normal karyotype, both at diagnosis and in samples obtained in complete remission(assessed by multiparametric flow cytometry) using the 10K SNP Array (Affymetrix). Both LOH and copy number analysis, as well as visualization of these analysis were performed by means of the dChip software (M. Lin et al., Bioinformatics (2004), 20:1233–40). A mean call rate of 96.8%. SNP array-based LOH analysis revealed that 4 patients presented large regions of homozygosity at diagnosis which were absent from samples in complete remission. In all four patients copy number analysis indicated no gross chromosomal losses or gains, as was confirmed by conventional cytogenetic analysis. Therefore, it can concluded that the LOH observed in these four patients was due to the presence of uniparental disomy. Simultaneous analysis of FLT-3 internal tandem duplications (FLT-3/ITD), FLT3- D835 mutations, NPM mutations and MLL rearrangements was performed using conventional molecular methods. Two of these patients (UPN2 and UPN12) had FLT-3/ITD in association with NPM mutations. UPN4 had a mutated form of NPM whereas in patient UPN16 FLT-3 and NPM genes were in the germ line configuration. All four cases were negative for MLL rearrangements and FLT-3-D835 mutations. These results suggest that NPM and FLT3 mutations may be associated with acquired somatic recombinations. It remains to be investigated whether there are loci preferentially involved by these events. Uniparental disomy and genetic lesions in normal karyotype AML Patient LOH FLT3 NPM D835 MLL UPN2 13q Mutated Mutated Germ line Germ line UPN4 6pter-p12.212q13.12-qter Germ line Mutated Germ line Germ line UPN12 2p Mutated Mutated Germ line Germ line UPN16 complex Germ line Germ line Germ line Germ line

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Quantification of Normal Cell Fraction and Copy Number Neutral LOH in Clinical Lung Cancer Samples Using SNP Array Data

PLoS ONE ◽

10.1371/journal.pone.0006057 ◽

2009 ◽

Vol 4 (6) ◽

pp. e6057 ◽

Cited By ~ 17

Author(s):

Hanna Göransson ◽

Karolina Edlund ◽

Maria Rydåker ◽

Markus Rasmussen ◽

Johan Winquist ◽

...

Keyword(s):

Lung Cancer ◽

Copy Number ◽

Normal Cell ◽

Snp Array ◽

Cell Fraction ◽

Array Data

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Evaluating Translocation Gene Fusions by SNP Array Data

Cancer Informatics ◽

10.4137/cin.s8026 ◽

2011 ◽

Vol 11 ◽

pp. CIN.S8026 ◽

Cited By ~ 4

Author(s):

Hong Liu ◽

Asher Zilberstein ◽

Pascal Pannier ◽

Frederic Fleche ◽

Christopher Arendt ◽

...

Keyword(s):

Cell Lines ◽

Cancer Cell ◽

Copy Number ◽

Target Genes ◽

Snp Array ◽

Tumor Development ◽

Cancer Cell Lines ◽

Genetic Alterations ◽

Genetic Aberrations ◽

Array Data

Somatic cell genetic alterations are a hallmark of tumor development and progression. Although various technologies have been developed and utilized to identify genetic aberrations, identifying genetic translocations at the chromosomal level is still a challenging task. High density SNP microarrays are useful to measure DNA copy number variation (CNV) across the genome. Utilizing SNP array data of cancer cell lines and patient samples, we evaluated the CNV and copy number breakpoints for several known fusion genes implicated in tumorigenesis. This analysis demonstrated the potential utility of SNP array data for the prediction of genetic aberrations via translocations based on identifying copy number breakpoints within the target genes. Genome-wide analysis was also performed to identify genes harboring copy number breakpoints across 820 cancer cell lines. Candidate oncogenes were identified that are linked to potential translocations in specific cancer cell lines.

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Rawcopy: Improved copy number analysis with Affymetrix arrays

10.1101/027409 ◽

2015 ◽

Author(s):

Markus Mayrhofer ◽

Bjorn Viklund ◽

Anders Isaksson

Keyword(s):

Copy Number ◽

Signal To Noise Ratio ◽

R Package ◽

Copy Number Analysis ◽

Genome Wide ◽

Microarray Sample ◽

Allele Specific ◽

Log Ratio ◽

Reference Samples ◽

Total Copy Number

Rawcopy is an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). It uses data from a large number of reference samples to produce log ratio for total copy number analysis and B-allele frequency for allele-specific copy number and heterozygosity analysis. Rawcopy achieves higher signal-to-noise ratio than commonly used free and proprietary alternatives, leading to improved identification of copy number alterations. In addition, Rawcopy visualises each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states.

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Genome-Wide Analysis of Copy Number Alterations/LOH/Allelic Imbalances in Non-Hodgkin Lymphoma Using Ultrahigh-Density SNP-Genotyping Microarrays with the Robust CNAG Algorithms.

Blood ◽

10.1182/blood.v106.11.420.420 ◽

2005 ◽

Vol 106 (11) ◽

pp. 420-420

Author(s):

Kumi Nakazaki ◽

Yasuhito Nannya ◽

Masashi Sanada ◽

Go Yamamoto ◽

Chiaki Aoyama ◽

...

Keyword(s):

Copy Number ◽

B Cell Lymphoma ◽

Genetic Alterations ◽

Snp Genotyping ◽

High Grade ◽

Copy Number Alterations ◽

Copy Number Analysis ◽

Genome Wide Analysis ◽

Genome Wide ◽

Allele Specific

Abstract Non-Hodgkin lymphomas (NHL) are hematopoietic malignancies originated from diversity of peripheral lymphoid organs. During the past two decades, there have been significant advances in the pathogenesis of NHL including identification of a number of genes associated with the disease-specific translocations and other genetic alterations. In view of cytogenetics, however, NHL frequently shows complex chromosomal abnormalities involving copy number alterations as well as other unbalanced translocations, many of which have not been unveiled at the molecular levels. Affymetrix® 100K/500K mapping arrays were originally developed for large-scale SNP typing required for genome-wide association studies, but the quantitative nature of the whole-genome amplification and hybridization used in these platforms also makes them powerful tools for genome-wide analysis of cancer genomes with use of uniformly distributed 116,204/520,000 SNP-specific probes. Moreover the use of SNP specific probes enables allele-specific copy number analysis that is totally impossible with other platforms. Here we developed the robust algorithms (Copy number analyzer for Affymetrix® GeneChip®; CNAG) for high-quality processing of 100K/500K data and analyzed a total of 72 NHL samples (61 primary samples including 34 diffuse large B-cell lymphoma, 18 follicular lymphoma and 11 cell lines including 3 adult T cell leukemia/ lymphoma) for genome-wide copy number alterations, LOH, and allelic imbalances at the resolutions of 23.6/5.4 kb. In 100K analysis, 34 homozygous deletions and 42 high-grade amplifications and other numerous copy number alternations and/or LOH, were identified together with possible gene targets as for some regions. 500K analysis disclosed even more subtle changes. Common overlapping alternations included deletions in 1p31.1 and 9p21.3, and 19p13.32 and high-grade amplifications in 3p14.2–p14.1,7q21.13–q21.3, and 20q11.21. Of particular importance is, however, the finding of otherwise undetected copy number neutral LOHs, which are revealed only by allele-specific copy-number analysis. In fact the copy number neutral LOHs represented a novel type of genetic abnormality in NHL because they were very frequent and found in more than 87% (20/23) of NHL cases examined with allele-specific copy number analysis, making a stark contrast to ALL, in which these abnormalities were rare. They typically involved chromosomal ends, indicating somatic recombinations are the potential mechanism of generating these abnormalities. Notably, there was a clear predisposition of the copy number neutral LOH to specific chromosomal loci including 1p, 1q, 6p, 9p, 17q, and 19p suggesting existence of relevant genes to NHL pathogenesis within these common regions. In conclusion, Affymetrix® SNP-genotyping microarrays and our CNAG algorithms provide a powerful platform of dissecting NHL genomes and could facilitate identification of the novel molecular mechanisms for lymphomagenesis.

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An Increased Frequency of Abnormalities Including Uniparental Disomy Is Detected by SNP Array Compared with Conventional Karyotype Analysis in Acute Myeloid Leukemia.

Blood ◽

10.1182/blood.v106.11.97.97 ◽

2005 ◽

Vol 106 (11) ◽

pp. 97-97 ◽

Cited By ~ 1

Author(s):

Manoj Raghavan ◽

Rosemary E. Gale ◽

Spyros Skoulakis ◽

Tracy Chaplin ◽

Gael Y. Molloy ◽

...

Keyword(s):

Copy Number ◽

Chromosomal Abnormalities ◽

Germ Line ◽

Snp Array ◽

Uniparental Disomy ◽

Data Set ◽

Array Data ◽

The Mean ◽

Homozygous Mutations ◽

Acute Myeloid

Abstract SNP array technology permits the simultaneous analysis of copy number and allelotype data. This approach has revealed the somatic acquisition of uniparental disomy (UPD) in approximately 20% of acute myeloid leukemias (AMLs) (Raghavan et al. Cancer Res2005;65:375–378). UPD, which mostly appears to be the consequence of mitotic recombination, cannot be detected by conventional analysis. We have conducted a pilot investigation of samples from the UK MRC AML 10 trial in order to confirm these findings in a larger data set from a large clinical trial. The Affymetrix 10K GeneChip Mapping Array was used to type DNA from 100 AML blast samples of which 87 produced arrays with call rates in excess of 90%. Analysis was performed using the genome orientated laboratory file (GOLF) system, an in-house software package designed to interpret SNP array data. Control germline DNA was not available for each AML and GOLF was used to create a control copy number experiment from the mean of 52 array data sets from normal tissue (blood and remission marrow). The copy number ratio was calculated for each SNP for each sample. In 44 samples the karyotype concurred with the SNP array results (excluding balanced translocations which cannot be detected by SNP array). In the other samples, 54 abnormalities were detected that were not seen in the karyotype (6 samples had no karyotype information). Nine were amplifications, 12 were deletions and 31 were UPDs (35%). Of the UPDs, 12 were either whole chromosome or extended to the most telomeric SNP, with the others therefore being interstitial changes. The mean size of an interstitial LOH was 13.3 Mb, with the smallest detected being 3.2 Mb. Recurrent chromosomal abnormalities not detected by giemsa banding are listed in table 1. Twenty samples that were regarded as normal karyotype by gene banding had abnormalities by SNP array. In three examples numerical karyotypic abnormalities were not seen on SNP array analysis (add4q, −8 and a hypodiploid AML). This may be because a minority clone of the AML cells had this karyotype. UPD is known to be associated with homozygous mutations in AML (Fitzgibbon et al. Cancer Res 2005; in press). In this series, two patients had UPD13, both with biallelic FLT3 internal tandem duplication mutations. However, this study has identified several new areas to look for potential homozygous mutations. Given that in this study germ-line comparison has not been made one should not rule out the possibility of some of the smaller abnormalities being copy number polymorphisms (Bailey et al. Science2005;297;1003–1007). However, consanguinity can probably be ruled out given the lack of widespread homozygosity. This study confirms the frequency of UPD and illustrates the potential of SNP arrays for highlighting novel genetic events in AML. Table 1: Recurrent chromosomal abnormalities not detected by gene banding Previously Undetected Abnormality Number UPD1p 2 Amplified 1p 2 UPD2p 2 Del7q 3 UPD8p 2 UPD11p 2 UPD11q 3 Amplified 12 3 Amplified 13 2 UPD16p 4 UPD16q 2 Del20q 2

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JAK2 V617F-Negative and MPL W515K/L-Negative Essential Thrombocythemia: A High Resolution SNP Array Study

Blood ◽

10.1182/blood.v122.21.5258.5258 ◽

2013 ◽

Vol 122 (21) ◽

pp. 5258-5258

Author(s):

Carla AL Assaf ◽

Els Lierman ◽

Timothy Devos ◽

Carlos Graux ◽

Johan Billiet ◽

...

Keyword(s):

Bone Marrow ◽

Essential Thrombocythemia ◽

Copy Number ◽

Conflicts Of Interest ◽

Myeloproliferative Neoplasms ◽

Snp Array ◽

Jak2 V617f ◽

Common Mutation ◽

Nicotinamide Phosphoribosyltransferase ◽

Array Data

Abstract Background JAK2 V617F is the most common mutation in essential thrombocythemia (ET), occurring in approximately 50 % of cases. Second to JAK2 V617F is MPL W515K/L, accounting for about 10 % of cases. The molecular cause of the remaining ET cases is still largely unknown. Aims We sought to investigate JAK2 V617F-negative and MPL W515K/L-negative ET for regions of copy number variations (CNV) and loss of heterozygosity (LOH). Methods We studied blood or bone marrow samples from a series of 64 JAK2 V617F-negative and MPL W515K/L-negative ET cases. They were subjected to 2.7M SNP array by Affymetrix, which has 2,761,979 copy number markers including 400,103 SNP markers. The array data were analyzed for recurrent CNVs with Array Studio (OmicSoft), and for individual CNVs or recurrent LOHs (≥3 Mbs) with the Chromosome analysis suite (ChAS, Affymetrix). Results Only 8 recurrent gains were identified, in 5/64 patients. Interestingly, the most common gain, occurring in 5 cases was a gain of chr7 q22.3, including the gene encoding Nicotinamide phosphoribosyltransferase (NAMPT). NAMPT is known to be overexpressed in several cancers such as multiple myeloma. It catalyzes the rate-limiting step of the nicotinamide adenine dinucleotide (NAD+) biosynthesis pathway. It is also required for cell growth and survival. We checked in the 5 patients for NAMPT amplification by quantitative PCR (qPCR) on genomic DNA in comparison to controls and by normalizing to ALB and RPPH1. We were able to validate the gain in 2/5 patients. The gain in these 2 patients was demonstrated to be acquired by qPCR of NAMPT in buccal swab DNA. Other recurrent gains involved regions of chromosomes 2, 5, 7, 12, 13, and 22. These gains included, amongst others, LCP1 on chr13 q14.3 and CYTIP on chr2 q24.1, occurring in 2/64 and in 3/64 respectively. We also checked for non-recurrent gains and losses in our cohort. This analysis generated a total of 8 CNVs in 6 different patients, comprising 5 regional gains in chromosomes 2, 8, 12, and 15 and 3 regional losses in chromosomes 5, 8 and 11. The array data were also analyzed for recurrent LOHs on ChAS, yielding 17 recurrent copy neutral LOHs (CN-LOH) in 35 patients (circos plot). The most common CN-LOH region was on chromosome 3 appearing in 8 patients. Other CN-LOH regions involved chromosomes 1, 2, 3, 4, 5, 6, 7, 10, 12, 15, and 17 and they occurred in 2-5/64 patients. However, as small regions of CN-LOH can be constitutional, we suspect that most of these CN-LOH regions are not acquired. The largest region of CN-LOH observed was 12 Mbs in size. Conclusions Previous studies in unselected series of BCR-ABL1-negative myeloproliferative neoplasms have shown that copy number alterations are rare in ET as well as in polycythemia vera. In this series of 64 JAK2 V617F-negative and MPL W515K/L-negative ET patients we found recurrent gains not reported previously in the database of genomic variants in only 8% of patients, and small areas of CN-LOH in ∼55% of cases. However, most of the latter probably are constitutional. Our SNP array study provides further evidence that gains, losses or CN-LOH of small genomic regions do not play an essential role in the pathogenesis of the majority of JAK2 V617F-negative and MPL W515K/L-negative ET. However, the low frequency of megakaryocytes and unknown level of clonal involvement of the myeloid compartment in JAK2 V617F-negative and MPL W515K/L-negative ET bone marrow remain a caveat. Next generation sequencing technology is expected to bring new insights on the molecular pathogenesis of this elusive ET subset. Circos plot showing the recurrent CN-LOHs Left half represents a total of 35 patients carrying recurrent CN-LOHs and the right half represents the chromosomes and their associated properties. Right outermost layer depicts 1+log-gene density (min, 1; max 42) where cancer, OMIM and other genes are colored in red, blue and green respectively. Right middle and innermost layers designates SNP density (blue, values < 0,02; gray values, <0,06; red values >0,06; max scale 0,013) and absolute SNP numbers (min, 1; max, 12074) per windows of 50kb. Each 5Mb distance is marked with a tick underneath the innermost layer. Links from each chromosome are colored differently. Regions that are more confined on the same chromosome are least transparent and regions that are shared by more patients are drawn on top of lesser links. Disclosures: No relevant conflicts of interest to declare.

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