Characterizing the allele-specific gene expression landscape in high hyperdiploid acute lymphoblastic leukemia with BASE.

Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations.

Childhood acute lymphoblastic leukaemia (ALL) may be divided into subgroups with different prognostic and clinical features based on the presence of specific acquired genetic aberrations. Cases with 51–67 chromosomes constitute the high hyperdiploid subgroup, characterized by non-random gains of chromosomes X, 4, 6, 10, 14, 17, 18, and 21 (Paulsson & Johansson, 2009). Additional genetic aberrations, such as microdeletions and point mutations, are sometimes present, but how they contribute to the leukemogenic process remains largely unknown. Functional in vitro studies of high hyperdiploid ALL are hampered by a lack of such cell lines, due to high hyperdiploid cells being exceedingly difficult to culture. In fact, to the best of our knowledge, only one cell line, MHH-CALL-2, is available from this ALL subtype. The aim of the present study was to perform genetic studies of MHH-CALL-2 to enable future use of this cell line as a model system for in vitro studies of high hyperdiploid childhood ALL. The MHH-CALL-2 cell line was established in 1993 from a peripheral blood sample obtained from a Caucasian 15-year-old female diagnosed with B-cell precursor ALL (Tomeczkowski et al, 1995). The karyotype has variably been described as 52,XX,+X,+10,+18,+18,+21,+21 (Tomeczkowski et al, 1995) and 52,XX,+8,+10,+18,+18,+21,+21 (The DSMZ database; http://www.dsmz.de/), i.e., with ambiguity regarding trisomy X/8. We performed G-banding analysis according to standard methods, showing a modal number of 51, with trisomies X and 18 and tetrasomy 21, and addition of a large marker chromosome. Multicolour-fluorescence in situ hybridization (M-FISH) using combined binary ratio labelling probes (Raap & Tanke, 2006) confirmed these gains and showed that the marker was a derivative chromosome 18 resulting from an unbalanced t(15;18) (Fig 1A, B); the latter was confirmed with whole chromosome painting probes (Applied Spectral Imaging, Neckarhausen, Germany). Because the translocation was unbalanced, single nucleotide polymorphism (SNP) array analysis (see below) enabled mapping of the breakpoints to 15q13.1 and 18q22.1 (Fig 1C). Taken together, the cell line MHH-CALL-2 was found to have the karyotype 51,XX,+X,+18,+der(18)t(15;18)(q13.1;q22.1),+21,+21. Neither +8 nor +10 were seen, in contrast to previous reports. Interphase FISH using a centromeric probe for chromosome 10 and the AML1/ETO (RUNX1/ RUNX1T1) probe set for chromosomes 8/21 (Abbott Molecular Inc., Des Plaines, IL, USA) confirmed disomy 8 and 10. Results of cytogenetic, fluorescence in situ hybridization (FISH), and SNP array analyses of MHH-CALL-2. (A, B) G-banding and multicolour-FISH showing the karyotype 51,XX,+X,+18,+der(18)t(15;18)(q13.1;q22.1),+21,+21. The der(18)t(15;18) is indicated by an arrow in panel A. (C) SNP array results. Top panels show the logR ratios, where copy number changes are shown as ratios above (gain) or below (loss) zero. Lower panels show the B allele frequency (BAF) values, indicating genotypes. Homozygous SNP reporters have values of 0 or 1; heterozygous SNP reporters have values of c. 0·5. The top chromosome is chromosome 18. Four copies are present from 18pter-q22.1, visible as increased logR ratios and retained heterozygosity ('2:2' tetrasomy). 18q22.1-qter is present in three copies, visible as increased logR ratios and skewed BAF values of c. 0·33 and c. 0·67. The lower chromosome is chromosome 9, which is a uniparental isodisomy, visible as logR ratios of c. 0 and complete loss of heterozygosity. A small homozygous deletion, including CDKN2A, is seen in 9p21, visible as decreased logR ratios and random BAF values due to the low signal intensities. SNP array analysis was done utilizing the Illumina 1M-quad bead Infinium BD BeadChip platform (Illumina, San Diego, CA, USA) as previously described (Paulsson et al, 2010). Copy number variants were excluded based on comparison with the Database of Genomic Variants (http://projects.tcag.ca/variation/). The analysis showed trisomy X and tetrasomies 18 [including one extra normal copy and the +der(18)t(15;18)] and 21, with doubling of both homologues ('2:2' tetrasomy). It also revealed what we would like to denote total 'UPIDity', i.e., all disomic chromosomes were uniparental isodisomies (UPIDs), detectable as complete loss of heterozygosity without concurrent copy number loss. Importantly, we have previously shown that only a minority of the disomies in high hyperdiploid ALL are UPIDs (Paulsson et al, 2010). Instead, universal UPIDity is suggestive of a near-haploid (23–29 chromosomes) or low hypodiploid (30–39 chromosomes) origin (Onodera et al, 1992; Paulsson & Johansson, 2009). Near-haploidy/low hypodiploidy occurs in <1% of childhood ALL (Harrison et al, 2004). More than half of such cases harbour a second clone with a chromosomal content in the high hyperdiploid range, where the original leukaemic cell has doubled all of its chromosomes (Harrison et al, 2004). In some patients, the original clone is no longer present and only the doubled clone, with a high hyperdiploid modal number, is seen. However these cases are generally considered to belong to the near-haploid/hypodiploid subgroup and are not 'true' high hyperdiploid ALL (Paulsson & Johansson, 2009). Thus, our findings suggest that MHH-CALL-2 should not be regarded as a high hyperdiploid cell line in spite of its chromosome number, but rather as a near-haploid. For patients, this distinction is important to make, as near-haploid childhood ALL has a dismal prognosis, with event-free survival rates of only c. 30% 3 years after diagnosis, in contrast to 75–80% for high hyperdiploid cases (Moorman et al, 2003; Harrison et al, 2004; Forestier et al, 2008). Reverse transcriptase-polymerase chain reaction was performed according to standard methods for ETV6/RUNX1 [t(12;21)(p13;q22)], BCR/ABL1 p190 and p210 [t(9;22)(q34;q11)], and TCF3/PBX1 [t(1;19)(q23;p13)] and Southern blot analysis was done using a probe for MLL (11q23). No abnormalities were detected, in line with the fact that these aberrations are categorized as ALL subgroups distinct from high hyperdiploidy. Furthermore, mutation analyses of FLT3, NRAS, KRAS, and PTPN11, performed as previously described (Paulsson et al, 2008), were all negative. The SNP array analysis showed that the breakpoints of the der(18)t(15;18) were at 27 636 979 bp (NCBI 36.1) in chromosome 15 and at 60 525 373 bp in chromosome 18; neither breakpoint was in a gene. The SNP array analysis also revealed a small homozygous deletion of the region 21 813 952–22 078 260 bp in 9p21 (Fig 1C), including CDKN2A, in line with the results from Mullighan et al (2007) showing that this gene is almost always lost in cases with <46 chromosomes. Taken together, our data suggest that the MHH-CALL-2 arose by a multistep process, with (i) initial near-haploidy with 26 chromosomes followed by (ii) CDKN2A deletion, (iii) doubling of the chromosomal content to 52 chromosomes, (iv) formation of a der(18)t(15;18) and (v) loss of an X chromosome. At least the first three steps must have occurred before establishment of the cell line, as the original leukaemia had 52 chromosomes. Considering the previously reported G-banding results, which deviate from ours by addition of a chromosome and no der(18) t(15;18), one may speculate that loss of one of four X chromosomes and acquisition of der(18)t(15;18) occurred after MHH-CALL-2 was established; i.e., they were not present in the patient. To summarize, the present study clearly shows that the MHH-CALL-2 cell line is in fact derived from a near-haploid childhood ALL, not a high hyperdiploid leukaemia as previously surmized. It is thus unsuitable as a model system for functional studies of the latter leukaemic subtype. Unfortunately, this also means that there is no high hyperdiploid ALL cell line available, hampering investigations of this large group of childhood ALL. The SNP array experiments were performed by Sciblu Genomics at Lund University, Lund, Sweden. This study was supported by grants from the Swedish Childhood Cancer Foundation, the Swedish Cancer Fund, and the Swedish Research Council.

Background: KMT2A-rearrangement is a characteristic finding in approximately 70% of infant acute lymphoblastic leukemia (ALL) cases. We previously utilized a computational screen to find that KMT2A-r infant ALL demonstrated somatic allele specific expression for 431 genes when compared to non-KMT2A-r samples (Abstract Number 3649, AACR 2019). The gene that exhibited the most differential allele specific expression (ASE) pattern was HOXA9. Here, we follow up that analysis with manual examination of additional infant ALL samples. Methods: We performed whole genome sequencing (WGS) and RNA sequencing (RNAseq) on peripheral blood or bone marrow samples from 48 infants with ALL (33 KMT2A-r cases and 15 non-KMT2A-r cases) treated on Children’s Oncology Group protocol AALL0631, at diagnosis (DX), at remission (MD), and at relapse (RL), if applicable. WGS data at MD was phased using a 1000 Genomes reference panel. HOXA9 expression was quantified in transcripts per million (TPM). Biallelic expression was manually calculated on the phased genome for samples with at least 1 germline single nucleotide polymorphism (SNP) within HOXA9 and at least 5 aligned RNAseq reads over the HOXA9 transcript. ASE was defined as minor allele fraction (MAF; allele fraction for the less prevalent allele) of ≤ 0.35. Whole genome bisulfite sequencing data and sequencing-derived copy number data were also analyzed to investigate possible explanations for HOXA9 ASE. Results: We identified diagnostic samples from 21 patients, 9 KMT2A-AFF1, 9 KMT2A-MLLT1, and 3 non-KMT2A-r, that passed manual filtering. Data included 5 patients with paired DX and RL samples. Of the 15 KMT2A-r samples unable to be analyzed for ASE, 13 lacked a SNP for phasing and 2 had &amp;lt; 5 reads. For the 12 non-KMT2A-r samples unanalyzable for ASE, 6 lacked a SNP and 6 had &amp;lt; 5 reads. Average HOXA9 expression was 15.17 TPM (range 0.01 to 44.34) in KMT2A-r samples and 2.91 TPM (range 0 to 29.29) in non-KMT2A-r samples. ASE of HOXA9 (MAF ≤ 0.35) was observed in 14 samples, 72% of KMT2A-r (13 of 18 samples) and 33% of non-KMT2A-r (1 of 3 samples). RL samples were found to have HOXA9 ASE in all cases with ASE of HOXA9 in the DX sample. Of the 18 KMT2A-r samples, 6 of 9 with KMT2A-AFF1 and 7 of 9 with KMT2A-MLLT1 demonstrated HOXA9 ASE. Frequency of HOXA9 ASE at diagnosis was similar between patients known to later relapse versus those known to remain in remission. Allele specific methylation, mono-allelic deletion, or copy-neutral loss of heterozygosity (cn-LOH) for HOXA9 were not observed in KMT2A-r nor non-KMT2A-r samples. Conclusion: Our expanded cohort supports the ASE of HOXA9 in KMT2A-r infant ALL. This phenomenon did not appear to segregate by KMT2A-r partner gene, nor could it be explained by allele specific methylation or copy number variation (e.g., deletion of one HOXA9 allele or cn-LOH). Overall, further investigation into a causal mechanism is needed. Citation Format: Sarah E. Mc Dermott, Byunggil Yoo, Warren A. Cheung, Emily Farrow, Bing Ge, Margaret Gibson, Patrick A. Brown, Erin Guest, Tomi Pastinen, Midhat S. Farooqi. HOXA9 demonstrates allelic imbalance in KMT2A-rearranged infant acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5725.

Recent large-scale genomic studies established the occurrence of multiple DNA sequence variants in genomes of healthy individuals that differ from the reference sequence. Among these variants mostly represented by germline single nucleotide polymorphisms disease-related alleles are detected including alleles which are associated with monogenic disorders, and putative deleterious genetic variants. Apart from functional significance of a particular variant and of a gene harboring it, the penetrance of these allelic variants depends on their expression level and can be determined by preferential expression of a particular allele, or allele-specific expression. It is estimated that 20–30 % of genes present in the human genome display allelic bias in a tissue-specific manner. Allele-specific expression is defined by a range of genetic and epigenetic mechanisms including cis-regulatory polymorphisms, allele-specific binding of transcription factors, allele-specific DNA methylation and regulation through non-coding RNA. Although the data on the issue are scarce, allele-specific expression has been reported to be implicated in several hereditary disorders including benign and malignant tumors of the large intestine. Recent studies that estimate allele-specific expression incidence in tumors and identify wide range of genes displaying allelic imbalance indicate that allele-specific expression might play a significant role in carcinogenesis. Eventually, estimation of transcriptional rate of allelic variants which cause dysfunction of oncogenes and tumor suppressors may prove to be essential for rational choice of antitumor therapeutic strategy. In this review, we outline the main concepts and mechanisms of allele-specific expression and the data on allelic imbalance in tumors.

Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool for understanding gene function across diverse cells. Recently, this has included the use of allele-specific expression (ASE) analysis to better understand how variation in the human genome affects RNA expression at the single-cell level. We reasoned that because intronic reads are more prevalent in single-nucleus RNA-Seq (snRNA-Seq), and introns are under lower purifying selection and thus enriched for genetic variants, that snRNA-seq should facilitate single-cell analysis of ASE. Here we demonstrate how experimental and computational choices can improve the results of allelic imbalance analysis. We explore how experimental choices, such as RNA source, read length, sequencing depth, genotyping, etc., impact the power of ASE-based methods. We developed a new suite of computational tools to process and analyze scRNA-seq and snRNA-seq for ASE. As hypothesized, we extracted more ASE information from reads in intronic regions than those in exonic regions and show how read length can be set to increase power. Additionally, hybrid selection improved our power to detect allelic imbalance in genes of interest. We also explored methods to recover allele-specific isoform expression levels from both long- and short-read snRNA-seq. To further investigate ASE in the context of human disease, we applied our methods to a Parkinson’s disease cohort of 94 individuals and show that ASE analysis had more power than eQTL analysis to identify significant SNP/gene pairs in our direct comparison of the two methods. Overall, we provide an end-to-end experimental and computational approach for future studies.

Many genetic variations in human populations are known, but genetic variability within healthy individuals is less familiar. Somatic mosaicism is the occurrence of genetically distinct cells within the same organism or tissue. Somatic mosaicism is well-known to occur in healthy cells of the immune system, and it has been frequently identified in disease, particularly cancer. A multi-step theory of cancer proposed in the 1970s1 and continually developed2 posits that genetic instability in precancerous cells leads to an accumulation of mutations that eventually give rise to tumorigenesis. Our results reveal new characteristics of intra-individual genetic instability.3 It remains widely assumed that healthy cells that arise from the same zygote contain identical genomes. This assumption underlies the research and diagnostic practice of using easily accessible blood or saliva DNA to perform genetic tests. A growing body of evidence counters that somatic genome rearrangements are relatively common. Age-related copy number variations (CNVs) in human blood cells were identified using SNP arrays.4 Retrotransposition5 was discovered in the human brain, although the extent of retrotransposition may have initially been overestimated.6 CNVs in DNA from somatic tissues7 were found using aCGH with low-resolution BAC arrays. BAC arrays suffer from reproducibility concerns and can detect variations only above ~50 kb. Structural variations starting at ~1 kb are thought to account for most of the variation in human genomes. Consequently, a great deal of somatic genomic variation likely remains understudied. We analyzed DNA from diverse tissues from six unrelated individuals for CNVs using high-resolution aCGH.3 The tissues were obtained during routine autopsy of subjects without known hereditary disorders or cancer. We identified 178 tissue-specific CNVs across 32 tissues; 73 were validated by a secondary method. The CNVs ranged from 2–184 kb, with the majority of events below 50 kb. Seventy-nine percent of the validated CNVs intersected genes. The mechanisms of somatic CNV formation cannot be definitively determined by aCGH. However, our breakpoint analyses revealed that somatic CNV breakpoints are enriched near microsatellite repeats. Commonly occurring somatic CNVs have implications for many aspects of biology. Seven somatic CNVs were identified in the same genomic region in more than one individual. We suspect that these locations are hotspots for somatic rearrangement. Liver, small intestine and pancreas were among the tissues with potential hotspot events. These tissues are derived from the endoderm germ layer. The hotspots perhaps play a role in the differentiation process. These same tissues also exhibited the most somatic CNVs overall. Compared with other tissues, such as brain, that displayed fewer somatic CNVs, these endoderm-derived tissues are known to experience greater cell proliferation and turnover. Conceivably, cell types with higher rates of division have more occasions to undergo genomic rearrangements. The subjects analyzed in our study were of middle to advanced age, and their dividing tissues are expected to have undergone many cell divisions. A comparison of DNA from somatic tissues of younger subjects with that from older subjects could reveal a relationship between a subject’s age and the degree of somatic variation. However, somatic variation may occur early in development. This would explain the occurrence of the CNV in a substantial fraction of the cells in a tissue sample. The aCGH signals suggest that there are not only genomic differences between tissues, but also within tissues. We attribute this, in part, to a portion of the tissues containing nonparenchymal cells from blood vessels and connective tissue that do not contain the particular CNVs. However, the signals indicate that the CNVs are heterogeneous throughout the parenchymal cells. Somatic CNVs potentially occur in many or all cells but are below the level of detection of aCGH. This hypothesis is supported by a recent study8 showing that many of the CNVs detected in iPS cells derived from human skin fibroblasts were also present at a low level in the primary fibroblast cultures. We speculate that highly deleterious CNVs make cells unviable and are never detected, while cells with neutral or advantageous CNVs persist and divide into clonal populations that can be detected. As technologies to analyze single cells improve, somatic genomic variation may be detected at the single-cell level. Our results indicate that somatic variations should be considered in biological sampling practices. “Normal” tissues from distant lineages, which are used for comparison, may identify somatic events that are not relevant to the disease state. Clinicians using blood and saliva DNA for diagnosis of genetic disorders may miss relevant somatic mutations in other tissues. Further analyses are necessary to determine the contribution of these somatic variations to biological variability and disease predisposition. Some of the somatic CNVs contain genes that have been shown in the literature to be expressed in the tissues we tested. Somatic CNVs that intersect tumor suppressors and/or oncogenes may directly induce tumorigenesis. Alternatively, somatic cells may acquire CNVs over many cell divisions, and the somatic CNV load creates genome instability or predisposition to malignant changes. Perhaps certain stages of development have greater protection from somatic variation or somatic variation provides variability that confers an advantage under certain environmental conditions. It remains to be seen how wide-reaching the implications of somatic genomic variation are on human biology.

Background: Catalase (CAT) is a key antioxidant gene expressed at high levels in most human tissues, including normal bronchial epithelial cells (NBEC). NBEC CAT expression is more disperse (more high and low extreme values) among subjects with cancer compared to controls. CAT shares this property with 14 other antioxidant and DNA repair genes comprised by the Lung Cancer Risk Test (LCRT) reported from this laboratory. We hypothesize that inter-individual variation in CAT regulation in NBEC is in part due to inter-individual variation at one or more cis-regulatory single nucleotide polymorphisms (SNPs). If so, this should manifest as inter-individual variation in allele-specific CAT expression in NBEC. Through funding in part from RC2 CA148572 and HL108016 we collected NBEC samples from over 500 subjects at risk for lung cancer. In this pilot study, we assessed allele-specific and total expression of multiple genes in NBEC samples from 85 subjects and assessed the genotype at putative cis-regulatory CAT SNP rs12807961 in gDNA from 95 subjects. Methods: RNA extracted from normal bronchial airway brush specimens of 85 subjects (26 cancer cases and 59 non-cancer controls) was reverse transcribed. Using next generation sequencing (NGS), allele-specific expression (ASE) was measured as allelic imbalance in each cDNA at three marker SNPs in the CAT coding region (rs1049982, rs769217, and rs704724) and one putative regulatory SNP (rs12807961) that was 4364 bases upstream of transcription start site, using gDNA as control. Specifically, each cDNA and matched peripheral blood cell gDNA sample was subjected to targeted competitive template multiplex PCR amplicon library generation followed by NGS (Blomquist et al, PLOS one, 2013) on Illumina Hiseq platform. The genotype at putative cis-regulatory SNP rs12807961 was assessed in gDNA from 95 subjects including those assessed for ASE (a total of 31 cancer cases and 64 non-cancer controls) using a TaqMan® SNP Genotyping Assay. Results: Among heterozygotes, there was significant inter-individual variation in cDNA allelic imbalance at rs1049982 (p&amp;lt;0.001, n=40) and rs769217 (p&amp;lt;0.001, n=28) as measured by F-test using matched gDNA controls. In this cohort there was insufficient number of heterozygotes at rs704724 (n=2) to assess ASE. Among all 95 subjects assessed for rs12807961 genotype, nine were homozygous minor allele at the rs12807961 CAT SNP. Of these, 7/31 cancer cases and 2/64 non-cancer controls were homozygous minor allele. This difference was significant by two-tailed Fisher exact test (P&amp;lt;0.05) following Bonferroni adjustment for multiple testing. Conclusions: These data support the hypothesis that cis-regulatory DNA variants contribute to inter-individual variation in CAT regulation in NBEC and that this is associated with lung cancer risk. Citation Format: Jiyoun Yeo, Xaiolu Zhang, Erin L. Crawford, James C. Willey. Inter-individual variation in allele specific expression of catalase (CAT) in normal bronchial epithelial cells and association of putative cis-regulatory CAT SNP rs12807961 with lung cancer risk. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4156. doi:10.1158/1538-7445.AM2014-4156

Clinical Impact of Copy Number Variation Revealed By Next Generation Sequencing in Acute Myeloid Leukemia

A large-scale behavior of allelic dropout and imbalance caused by DNA methylation changes in an early-ripening bud sport of peach.

Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian cell. Here we address the process by which CNVs become depleted of UCEs. We begin by showing that depletion for UCEs characterizes the most recent large-scale human CNV datasets and then find that even newly formed de novo CNVs, which have passed through meiosis at most once, are significantly depleted for UCEs. In striking contrast, CNVs arising specifically in cancer cells are, as a rule, not depleted for UCEs and can even become significantly enriched. This observation raises the possibility that CNVs that arise somatically and are relatively newly formed are less likely to have established a CNV profile that is depleted for UCEs. Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state. In support of this latter explanation, somatic CNVs that are not associated with disease are depleted for UCEs. Finally, we show that it is possible to observe the CNVs of induced pluripotent stem (iPS) cells become depleted of UCEs over time, suggesting that depletion may be established through selection against UCE-disrupting CNVs without the requirement for meiotic divisions.

DNA copy number variations (CNVs) comprise a recently discovered element of genetic variation that affects a greater cumulative fraction of the genome than single-nucleotide polymorphisms (SNPs). This review discusses current understanding of the characteristics of CNVs in the human genome and explores the emerging discoveries of both constitutional and somatic CNVs in an ever-expanding variety of human cancers. The advent of high-resolution SNP arrays has made it possible to identify CNVs. Characterization of widespread constitutional CNVs offers insight into their role in disease susceptibility, whereas somatic CNVs identify regions of the genome involved in disease phenotype. The role of CNVs in cancer has only emerged in the last 2 years, with constitutional CNVs originally being observed in the Li-Fraumeni cancer susceptibility syndrome, and more recently in neuroblastoma. It is not yet known how common or how functionally relevant CNVs will be to the process of carcinogenesis. Nonetheless, the inherent instability and structural variability that characterize cancer cell genomes make this form of genetic variation particularly intriguing to the study of cancer.

Somatic Structural Variations in Pediatric High Hyperdiploid Acute Lymphoblastic Leukemia Revealed by Paired-End Parallel Sequencing

Recent studies have unveiled copy number variants (CNVs) as an important source of genetic variation. Many of these CNVs contain coding sequences, which have been shown to be dosage sensitive. Evidence is accumulating that certain CNVs have impact on susceptibility to human diseases such as HIV infection and autoimmune diseases, as well as on adaptability to environmental conditions or nutrition. The possible role and impact of CNVs on cancer development and progression is only now emerging. In this review we look into the role of CNVs and their associated genomic structural features in relation to the formation of chromosome alterations in cancer cells and evolutionary genomic plasticity, as well as the de novo occurrence of known or putative CNVs as somatic events during oncogenesis. The role of germline CNVs in cancer predisposition is still largely unexplored. A number of observations seem to warrant the importance of further studies to elucidate the impact of these variants in the early steps of carcinogenesis.

Allele-specific expression (ASE) is a useful way to identify cis-acting regulatory variation, which provides opportunities to develop new therapeutic strategies that activate beneficial alleles or silence mutated alleles at specific loci. However, multiple problems hinder the identification of ASE in next-generation sequencing (NGS) data. We developed cisASE, a likelihood-based method for detecting ASE on single nucleotide variant (SNV), exon and gene levels from sequencing data without requiring phasing or parental information. cisASE uses matched DNA-seq data to control technical bias and copy number variation (CNV) in putative cis-regulated ASE identification. Compared with state-of-the-art methods, cisASE exhibits significantly increased accuracy and speed. cisASE works moderately well for datasets without DNA-seq and thus is widely applicable. By applying cisASE to real datasets, we identified specific ASE characteristics in normal and cancer tissues, thus indicating that cisASE has potential for wide applications in cancer genomics. cisASE is freely available at http://lifecenter.sgst.cn/cisASE CONTACT: biosinodx@gmail.com or yxli@sibs.ac.cnSupplementary information: Supplementary data are available at Bioinformatics online.

Genome-Wide Analysis of Allele-Specific Expression Genes in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia