SNP Microarray Research Articles

47. Serendipitous identification of meiotic crossover events in struma ovarii tumors by whole genome SNP microarray analysis

Germ cell divisions, Meiosis I and II, specifically produce haploid gametes (2n→n) required for sexual reproduction. Reciprocal crossing over between homologues of a chromosome pair is a fundamental event ensuring genomic contribution from each parent in a gamete. Using the OncoScan SNP microarray, we have identified and quantified the number and location of crossovers distributed throughout the genome. This exposure of crossovers was noted serendipitously while studying the genetic constitution of tumors of ovarian origin (struma ovarii). In tumors displaying segmental whole genome homozygosity, the precise locations of transitions from homozygosity to heterozygosity could be visualized and represent the sites of crossovers. Our analysis and data from 7 struma ovarii specimens revealed that the number of total whole genome crossovers events ranged from 41 to 99 events. Also, the total number of crossovers (summed by chromosome across these 7 struma ovarii samples) in Group A chromosomes (1–3) ranged from 23 to 41 events, in Group B (4–5) from 24 to 34 events, in Group C (6–12, X) from 17 to 25 events, in Group D (13–15) from 12 to 20 events, in Group E (16–18) from 15 to 19 events, in Group F(19–20) from 14 to 16 events, and in Group G (21–22) from 7 to 10 events. Moreover, the data revealed a) the frequency of the crossover events was directly proportional to the length of the chromosome, b) an increased (p < 0.01) number of genome-wide crossovers in the “p” arm versus the “q” arm, c) the percent homozygosity between individual chromosomes ranged between 20 and 50%, and no correlation between the percent homozygosity per chromosome, between chromosome arms, or chromosome length.

16. Australian AIEOP-BFM 2009 acute lymphoblastic leukaemia high-risk findings – Enrichment of IKZF1 deletions and other curious findings

Background: Whole genome high density (HD) SNP microarray analysis provides valuable insights into the cancer genome, unveiling important prognostic findings and therapeutic targets.

Abstract 3997: Somatic mutational processes in the cancerization field of the normal-appearing airway reveal early drivers in the development of non-small cell lung cancer

Abstract BACKGROUND: There are very few strategies to treat non-small cell lung cancer (NSCLC) at its primitive stages largely due to our poor understanding of molecular aberrations in development of the malignancy and that would be ideal targets for early treatment. Work from our group and others revealed that visually "normal" airway cells carry alterations (e.g. expression and copy number changes) that are characteristic of the nearby lung tumor, signifying a "field of cancerization" that is pertinent to the pathobiology of the tumor. Yet, the landscape of driver alterations in the cancerization field of the normal-appearing airway remains largely unexplored. METHODS: 409 cancer-associated genes were surveyed by deep targeted sequencing in tumor adjacent (small airways) and distant (mainstem bronchi/large airways, nasal epithelia, normal lung parenchyma) normal-appearing tissues as well as in multi-region tissues from paired tumors contrasting events in blood, for a total of 500 samples from 48 patients with early-stage NSCLC (11 squamous cell carcinomas and 37 adenocarcinomas). Somatic point mutations were interrogated by aggregating multiple mutation callers. Mutation were then paired with our recent study of genome-wide copy number alterations (CNAs) inferred from high-density whole-genome SNP microarrays. RESULTS: We identified somatic point mutations in 76 normal-appearing field samples (75% of patients) which were overall concordant with profiles in corresponding NSCLCs. Somatic mutation signatures associated with smoking, APOBEC activity and DNA mismatch repair were common to both airway field samples and NSCLCs from smoker cases. Airway field mutation burdens, while varied, increased significantly with proximity to the tumor. Most field mutations were observed in tumor-adjacent small airways (from 31 patients) some of which were in known drivers such as TP53, KEAP1, STK11 and KRAS. Somatic mutations were also identified in more distant normal samples including large airways (TP53, SETD2, CDKN2A), normal lung parenchyma (RB1, RET) and nasal epithelium (AKT1). We then integrated point mutation and CNA data and found "two-hit" gene alteration patterns in airway field samples that were consistent with their matched NSCLCs, including point mutated gene/CNA pairs such as KEAP1 and STK11/19p loss, TP53/17p loss and KRAS/12p gain. Some additional cases exhibited single hits (e.g., TP53) in their airway field progressing to "two-hits" (e.g., TP53/17p loss) in the matched NSCLC. CONCLUSIONS: Our integrative high-throughput sequence and genome-wide SNP analyses implicate early mutational processes and putative drivers in the progression of the mutagenized "normal" airway field of cancerization to NSCLC thus offering insights into strategies for interception via early detection and personalized prevention. Citation Format: Smruthy Sivakumar, Yasminka Jakubek, F Anthony San Lucas, Wenhua Lang, Christina McDowell, Zachary Weber, Carmen Behrens, Neda Kalhor, Cesar Moran, Randa El-Zein, Gareth Davies, Junya Fujimoto, Reza Mehran, Stephen G. Swisher, Jing Wang, Jerry Fowler, Steven Dubinett, Avrum E. Spira, Erik Ehli, Ignacio I. Wistuba, Paul Scheet, Humam Kadara. Somatic mutational processes in the cancerization field of the normal-appearing airway reveal early drivers in the development of non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3997.

HuH-7 reference genome profile: complex karyotype composed of massive loss of heterozygosity

Human cell lines represent a valuable resource as in vitro experimental models. A hepatoma cell line, HuH-7 (JCRB0403), has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. However, an accurate genome profile, which can be served as a reliable reference, has not been available. In this study, we performed M-FISH, SNP microarray and amplicon sequencing to characterize the cell line. Single cell analysis of metaphases revealed a high level of heterogeneity with a mode of 60 chromosomes. Cytogenetic results demonstrated chromosome abnormalities involving every chromosome in addition to a massive loss of heterozygosity, which accounts for 55.3% of the genome, consistent with the homozygous variants seen in the sequence analysis. We provide empirical data that the HuH-7 cell line is composed of highly heterogeneous cell populations, suggesting that besides cell line authentication, the quality of cell lines needs to be taken into consideration in the future use of tumor cell lines.

33. SNP microarray autozygosity-directed mutation assessment of children and families with heritable retinal dystrophies in Costa Rica; identification of autosomal recessive mutations and one copy number variant

33. SNP microarray autozygosity-directed mutation assessment of children and families with heritable retinal dystrophies in Costa Rica; identification of autosomal recessive mutations and one copy number variant

Insight into the mechanisms and consequences of recurrent telomere capture associated with a sub-telomeric deletion.

A complex mosaicism of the short arm of chromosome 1 detected by SNP microarray analysis is described in a patient presenting a 4-Mb 1p36 terminal deletion and associated phenotypic features. The array pattern of chromosome 1p displayed an intriguing increase in divergence of the SNP heterozygote frequency from the expected 50% from the centromere towards the 1p36 breakpoint. This suggests that various overlapping segments of UPD were derived by somatic recombination between the 1p homologues. The most likely explanation was the occurrence of a series of events initiated in either a gamete or an early embryonic cell division involving a 1pter deletion rapidly followed by multiple telomere captures, resulting in additive, stepped increases in frequency of homozygosity towards the telomere. The largest segment involved the entire 1p, and at least four other capture events were observed, indicating that at least five independent telomere captures occurred in separate cell lineages. The determination of breakpoint position by detection of abrupt changes in B-allele frequency using a moving window analysis demonstrated that they were identical in blood and saliva, the tissues available for analysis. We developed a model to explain the interaction of parameters determining the mosaic clones and concluded that, while number, size, and position of telomere captures were important initiating determinants, variation in individual clone frequencies was the main contributor to mosaic differences between tissues. All previous reports of telomere capture have been restricted to single events. Other cases involving multiple telomere capture probably exist but require investigation by SNP microarrays for their detection.

A remark on copy number variation detection methods.

Copy number variations (CNVs) are gain and loss of DNA sequence of a genome. High throughput platforms such as microarrays and next generation sequencing technologies (NGS) have been applied for genome wide copy number losses. Although progress has been made in both approaches, the accuracy and consistency of CNV calling from the two platforms remain in dispute. In this study, we perform a deep analysis on copy number losses on 254 human DNA samples, which have both SNP microarray data and NGS data publicly available from Hapmap Project and 1000 Genomes Project respectively. We show that the copy number losses reported from Hapmap Project and 1000 Genome Project only have < 30% overlap, while these reports are required to have cross-platform (e.g. PCR, microarray and high-throughput sequencing) experimental supporting by their corresponding projects, even though state-of-art calling methods were employed. On the other hand, copy number losses are found directly from HapMap microarray data by an accurate algorithm, i.e. CNVhac, almost all of which have lower read mapping depth in NGS data; furthermore, 88% of which can be supported by the sequences with breakpoint in NGS data. Our results suggest the ability of microarray calling CNVs and the possible introduction of false negatives from the unessential requirement of the additional cross-platform supporting. The inconsistency of CNV reports from Hapmap Project and 1000 Genomes Project might result from the inadequate information containing in microarray data, the inconsistent detection criteria, or the filtration effect of cross-platform supporting. The statistical test on CNVs called from CNVhac show that the microarray data can offer reliable CNV reports, and majority of CNV candidates can be confirmed by raw sequences. Therefore, the CNV candidates given by a good caller could be highly reliable without cross-platform supporting, so additional experimental information should be applied in need instead of necessarily.

A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour.

High-density SNP microarrays ("SNP chips") are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high-density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.

The effect of QTL-rich region polymorphisms identified by targeted DNA-seq on pig production traits

The aim of the present study was to analyse the effect of PLCD4, PECR, FN1 and PNKD mutations on pig productive traits and tested the usefulness of targeted enrichment DNA sequencing method as tool for preselection of genetic markers. The potential genetic markers for pig productive traits were identified by using targeted enrichment DNA sequencing of chromosome 15 region that is QTL-rich. The selected mutations were genotyped by using HRM, Sanger sequencing and PCR-ACRS methods. The association study was performed by using GLM model in SAS program and included over 500 pigs of 5 populations maintained in Poland. The variation (C/T) of PLCD4 gene affected feed conversion, intramuscular fat and water exudation. The PNKD mutations were associated with texture parameters measured after cooking. In turn, the variation rs792423408 (C/T) in the FN1 gene influenced toughness measured in semimembranosus muscle and growth traits that was observed particularly in Duroc breed. Summarizing, the investigated gene variants delivered valuable information that could be used during developing SNP microarray for genomic estimated breeding value procedure in pigs. Moreover, the study showed that the TEDNA-seq method could be used to preselect the molecular markers associated with pig traits. However, the further association study that included large number animal populations is necessary.

The Application of SNP Microarray Technique in Fetal Central Nervous System Abnormality

The Application of SNP Microarray Technique in Fetal Central Nervous System Abnormality

Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays

BackgroundThe recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray.ResultsOverall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input.ConclusionsOur results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA.

Genetic markers of canine hip dysplasia

Canine hip dysplasia is a complex skeletal malformation caused by genetic and environmental factors. The prevalence of hip dysplasia in different canine breeds ranges widely, from 1% (for Whippet and Borzoi) to over 70% (for Bulldog and Pug). These differences indicate the presence of genetic variants predisposing to or preventing this disorder in gene pools of particular breeds. The importance of genetic factors is also confirmed by a high coefficient of heritability (h2) of canine hip dysplasia, which for most breeds oscillates around 0.5 – 0.6. Application of modern genomic methods, that is, mainly genome scanning (based previously on microsatellite markers and currently on SNP microarrays) has led in recent years to the identification of potential genetic markers associated with this disorder. Such studies were carried out mostly in two breeds: Labrador retriever and German shepherd. Some of the markers were found in the vicinity of genes involved in skeletal development. Following these achievements, the use of some markers has been suggested for early risk diagnosis of hip dysplasia. This shows that molecular testing is becoming important for not only monogenic, but also polygenic canine diseases and disorders. Identification of genetic markers associated with predisposition to hip dysplasia offers an opportunity for an early risk evaluation of this disorder (prior to its first signs). Moreover, it facilitates effective breeding selection aimed at eradicating undesirable genetic variants from the gene pool of a given breed..

Сравнительный обзор методов диагностики хромосомных аномалий у плодов с пороками развития и/или эхографическими маркерами хромосомной патологии

The article presents a comparative analysis of methods used for the diagnosis of genetic pathology in fetuses with malformations and / or developmental abnormalities. The standard cytogenetic analysis of the karyotype is most widely implemented and used, however, the low resolution of this method in 8Mb does not allow for the detection of microdeletions and microduplications, which in turn in 5-6% of cases are the causes of malformations and / or developmental abnormalities in the fetus. When using chromosomal microarray analysis (CMA) it increases the diagnostic efficacy of prenatal diagnosis, which allows making a diagnosis in a timely manner, determining the prognosis for the life of the child after birth. The choice of method for diagnosing genetic pathology in fetuses with congenital malformations and / or developmental abnormalities is currently not regulated and is often based on the technical capabilities of the laboratory. At the moment, a large amount of data has been accumulated confirming the effectiveness of the use of SNP microarrays compared to classical cytogenetic methods.

Identification of a c.544C>T mutation in WDR34 as a deleterious recessive allele of short rib-polydactyly syndrome

ObjectiveSingle-nucleotide polymorphism (SNP) microarrays and whole-exome sequencing (WES) are tools to precisely diagnose rare autosomal recessive (AR) diseases. In this study, SNP chip and WES were used to identify a mutated location in WDR34 in a baby born to consanguineous parents. Case reportThe baby, born at 36 gestational weeks had a small thoracic cage, symmetric short proximal bones, and polydactyly. Radiography showed short ribs with reduced lung volume and pulmonary opacities, compatible with asphyxiating thoracic dystrophy or short rib-polydactyly syndrome (SRPS). At 4 months of age, she died of pulmonary hypoplasia and sepsis. SNP microarray and evaluation tool confirmed WDR34 as the candidate gene. WES detected an AR mutation at c.554C > T [p.Arg182Trp] in WDR34. ConclusionThis study was the first to identify c.544C > T [p.Arg182Trp] mutation in WDR34 in a patient with SRPS. According to the database, the homozygous mutation of c.544C > T in WDR34 was deleterious and the prevalence of heterozygous mutation was relatively higher in Asian population. More studies of this mutation in patients with SRPS are required.

P1-224 - Chromothripsis-like pattern in multiple myeloma

Multiple myeloma is a malignant disease caused by an abnormal proliferation of plasma cells. In clinical classification, prediction of risk includes chromosomal abnormality, beta-2 microglobulin (b2MG), albumin, and bone marrow plasma cell (%). Recently, the term of chromothripsis has been emerged, and many studies have shown that association of chromothripsis with prognosis in many cancers, however, few studies have examined chromothripsis in myeloma. Here, we studied the relationship between chromothripsis-like pattern and treatment resistance and prognosis. We analyzed bone marrow samples of 32 patients who were diagnosed as myeloma by Affymetrix CytoScan 750k SNP microarray. Then, we analyzed chromothripsis-like pattern using Chromosome analysis suite (ChAS) program. Treatment response of patients were divided into two groups (sensitive/resistance) according to international myeloma working group (IMWG). The frequency of chromosomal aberrations and chromothripsis-like pattern were compared in different clinical groups. There were significant mosaic gain at chromosome (chr) 1 (P = 0.0133) and loss at chr6 (P = 0.0376) and chr11 (P = 0.0402) in resistance group patients. Through comparing two groups by overall survival [OS, median=22.1 months], longer survival group showed additional gain on the chr3, 9 and mosaic gain on chr8. Shorter survival group had more gain on chr7, 22 and loss on chr17 and 18. Chromothripsis-like pattern was observed in sensitivity (N = 5) more than resistance (N = 1). In comparison of two groups according to OS, however, there was no significant difference (N = 3, respectively). Our study showed similar result as previous studies by showing chromosomal aberration on chr1, 3 and 12. Furthermore, we observed chromothripsis-like pattern on chromosome 6 and 7 frequent in sensitivity group. (This study was supported by National Research Foundation of Korea grant funded by the Korea government (MSIP) (No. 2014R1A2A2A01002553).)

Preliminary analysis of numerical chromosome abnormalities in reciprocal and Robertsonian translocation preimplantation genetic diagnosis cases with 24-chromosomal analysis with an aCGH/SNP microarray.

The aim of this study was to determine whether an interchromosomal effect (ICE) occurred in embryos obtained from reciprocal translocation (rcp) and Robertsonian translocation (RT) carriers who were following a preimplantation genetic diagnosis (PGD) with whole chromosome screening with an aCGH and SNP microarray. We also analyzed the chromosomal numerical abnormalities in embryos with aneuploidy in parental chromosomes that were not involved with a translocation and balanced in involved parental translocation chromosomes. This retrospective study included 832 embryos obtained from rcp carriers and 382 embryos from RT carriers that were biopsied in 139 PGD cycles. The control group involved embryos obtained from age-matched patient karyotypes who were undergoing preimplantation genetic screening (PGS) with non-translocation, and 579 embryos were analyzed in the control group. A single blastomere at the cleavage stage or trophectoderm from a blastocyst was biopsied, and 24-chromosomal analysis with an aCGH/SNP microarray was conducted using the PGD/PGS protocols. Statistical analyses were implemented on the incidences of cumulative aneuploidy rates between the translocation carriers and the control group. Reliable results were obtained from 138 couples, among whom only one patient was a balanced rcp or RT translocation carrier, undergoing PGD testing in our center from January 2012 to June 2014. For day 3 embryos, the aneuploidy rates were 50.7% for rcp carriers and 49.1% for RT carriers, compared with the control group, with 44.8% at a maternal age <36years. When the maternal age was ≥36years, the aneuploidy rates were increased to 61.1% for rcp carriers, 56.7% for RT carriers, and 60.3% for the control group. There were no significant differences. In day 5 embryos, the aneuploidy rates were 24.5% for rcp carriers and 34.9% for RT carriers, compared with the control group with 53.6% at a maternal age <36years. When the maternal age was ≥36years, the aneuploidy rates were 10.7% for rcp carriers, 26.3% for RT carriers, and 57.1% for the control group. The cumulative aneuploidy rates of chromosome translocation carriers were significantly lower than the control group. No ICE was observed in cleavage and blastocyst stage embryos obtained from these carriers. Additionally, the risk of chromosomal numerical abnormalities was observed in each of the 23 pairs of autosomes or sex chromosomes from day 3 and day 5 embryos. There was not enough evidence to prove that ICE was present in embryos derived from both rcp and RT translocation carriers, regardless of the maternal age. However, chromosomal numerical abnormalities were noticed in 23 pairs of autosomes and sex chromosomes in parental structurally normal chromosomes. Thus, 24-chromosomal analysis with an aCGH/SNP microarray PGD protocol is required to decrease the risks of failure to diagnose aneuploidy in structurally normal chromosomes.

P16.05: The influence of chromosomal microarray and NIPT on the diagnostic yield in 6,811 high‐risk pregnancies without ultrasound anomalies

Prenatal diagnostics has been impacted by technological changes in the past decade, which have affected the diagnostic yield. The aim of this study was to evaluate the impact of SNP array and non-invasive prenatal testing (NIPT) on the diagnostic yield and the number of invasive tests in our centre. The frequency of pathogenic fetal unbalanced chromosome aberrations was studied in 6811 high risk pregnancies without ultrasound anomalies referred for prenatal testing in 2009-2015 due to advanced maternal age, abnormal first trimester screening results (with nuchal translucency < 3.5mm) or recurrence risk for chromosome aberration. Chromosomal SNP microarray analysis replaced karyotyping in 2012 and since 2014 a choice between NIPT and diagnostic testing with microarray was offered to women with an increased risk for common aneuploidy (as a part of a national TRIDENT study). The introduction of microarray led to an additional yield of submicroscopic pathogenic chromosome aberrations in 1.9% in fetuses without ultrasound anomalies. The introduction of NIPT led to a decrease of invasive tests, but also of the diagnostic yield. Supporting information can be found in the online version of this abstract Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

The human vascular endothelial cell line HUV-EC-C harbors the integrated HHV-6B genome which remains stable in long term culture

Human herpes virus 6 (HHV-6) is a common human pathogen that is most often detected in hematopoietic cells. Although human cells harboring chromosomally integrated HHV-6 can be generated in vitro, the availability of such cell lines originating from in vivo tissues is limited. In this study, chromosomally integrated HHV-6B has been identified in a human vascular endothelial cell line, HUV-EC-C (IFO50271), derived from normal umbilical cord tissue. Sequence analysis revealed that the viral genome was similar to the HHV-6B HST strain. FISH analysis using a HHV-6 DNA probe showed one signal in each cell, detected at the distal end of the long arm of chromosome 9. This was consistent with a digital PCR assay, validating one copy of the viral DNA. Because exposure of HUV-EC-C to chemicals did not cause viral reactivation, long term cell culture of HUV-EC-C was carried out to assess the stability of viral integration. The growth rate was altered depending on passage numbers, and morphology also changed during culture. SNP microarray profiles showed some differences between low and high passages, implying that the HUV-EC-C genome had changed during culture. However, no detectable change was observed in chromosome 9, where HHV-6B integration and the viral copy number remained unchanged. Our results suggest that integrated HHV-6B is stable in HUV-EC-C despite genome instability.

Abstract 2451: Genomic wide microarray analysis identifies novel copy number alterations in adult acute myeloid leukemia

Abstract Introduction: Novel array-based technique as SNP microarray can detect losses or gains of chromosomic material, which could be predictive of response and can help define therapeutic strategies. The aim of this study is to improve conventional cytogenetic analysis and identify new genetic alterations relevant to leukemogenesis, by a SNP array-based genotyping approach. Materials and Methods: We performed SNP 6.0 or Cytoscan HD (Affymetrix) in 235 Acute Myeloid Leukemia (AML) patients at diagnosis. Seventy-eight/235 samples were also performed by Whole Exome Sequencing, WES (HiSeq,Illumina). SNP Array data were analyzed by Nexus Copy Number v8.0 (BioDiscovery) and R Core Team. Results: Copy Number Alterations (CNAs) were scattered across all chromosomes and all pts showed CNA events. SNP array analysis showed that several genes were preferentially deleted, including MRPS5 (14.8%), PHF6 (9.3%), SCAPER (7.2%), CASK (5.9%), WNK (4.6%), STAG2 (4.2%), LRRK1 (3.4%), PALB2 (3.4%), while the genes preferentially amplified were RABL2B (16.1%), NF2 (10.2%), NBPF9 (7.6%), JAK2 (6.8%), RB1, NF1 and KMT2A (4.2%), PTEN (3.4%), TP73 and SMAD2 (2.5%). Single-copy losses and deletions were enriched (p&amp;lt;.001) for genes mapping into the following pathways: aberrant PD-1 signaling, loss of function of SMAD4 in cancer and SMAD4 MH2 Domain mutants in cancer. The functional pathways significantly (p&amp;lt;.001) deregulated in our cohort with single copy gain and homozygous amplification were: regulation of transcription and nucleic acid, negative regulation of metabolic processes, constitutive signaling by aberrant PI3K in cancer and PI3K/AKT network. Finally, in order to define driver alterations, we correlate deletions and losses with mutational data. Interestingly, we found losses which are also targeted by mutations (BRCA2, LRRK1). Moreover, some deleted genes, as CASK, CDK6 and MAPT, were involved in pathways affected by genomic mutations (CASK deletion and MPP6 mutation, CDK6 deletion and PPM1D mutation, MAPT deletion and SPAG5 mutation). Conclusion: We have identified new CNAs and pathways involving novel potential leukemia-related genes. Our results suggest that the comparison between SNP and WES data could provide important findings on prognosis of AML patients. Minimal deleted regions of genes implicated in deregulated pathways deserve further investigation in order to identify new candidate genes which could be relevant AML biomarkers. Acknowledgements: ELN,AIL,AIRC,progetto Regione-Università 2010-12 (L. Bolondi),FP7 NGS-PTL project,HARMONY. Citation Format: Maria Chiara Fontana, Giovanni Marconi, Cristina Papayannidis, Eugenio Fonzi, Giorgia Simonetti, Antonella Padella, Anna Ferrari, Emanuela Ottaviani, Silvia Lo Monaco, Stefania Paolini, Simona Soverini, Giovanni Martinelli. Genomic wide microarray analysis identifies novel copy number alterations in adult acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2451. doi:10.1158/1538-7445.AM2017-2451

Abstract 2463: Tumor profiling of separated carcinomatous and sarcomatous components from uterine carcinosarcoma biopsies provides insights into their development

Abstract Uterine carcinosarcoma (UCS) is a rare and aggressive form of uterine cancer. It is bi-phasic, exhibiting histological features of both malignant epithelial (carcinomatous) and mesenchymal (sarcomatous) elements. Studies have indicated that UCS arises from sarcomatous differentiation of high-grade carcinoma while others have suggested a bi-clonal nature. Given these differences, we sought to separate the carcinoma and sarcoma elements of UCS to try to understand their molecular differences and gain further insights into how these tumors develop. We macrodissected carcinomatous, sarcomatous, and normal cells from formalin fixed paraffin embedded (FFPE) uterine samples of 10 UCS patients. DNA and RNA were isolated and extracted using the Qiagen AllPrep DNA/RNA FFPE kit. Whole-genome SNP microarrays and deep sequencing of 26 cancer genes was performed, using the Illumina Infinium OmniExpressExome array and the TruSight Tumor panel respectively. Illumina HiSeq mRNA sequencing was also performed to quantify gene expression. The genomic allelic imbalance (AI) profiling, called from the SNP data by hapLOH, showed that sarcoma samples were more aberrant than their carcinoma counterparts (abstract 131, AACR 2016). From the targeted sequencing, the Illumina Amplicon-DS Somatic Variant Caller was employed to call somatic mutations. Mutations were identified in TP53 in both the sarcoma and carcinoma samples of all 10 patients. Frequently mutated genes included APC, EGFR, MET and MSH6 which were found in 60-80% of the patients. Genes mutated in less than 50% of the patients included PTEN, KRAS, KIT, FBXW7, PIK3CA, FGFR2, and CTNNB1. Current results showed no association of a mutated gene to either the sarcoma or carcinoma component of UCS. RSEM, STAR and EBSeq were applied to the RNA-seq data for gene expression quantification. Approximately 2500 genes were identified as being differentially expressed (DE) between normal and carcinoma samples. Just over 4000 genes were identified as being DE between normal and sarcoma samples. 75% of the DE genes in the carcinoma were also identified in the sarcoma. Using DAVID functional annotation tool, we characterized these gene sets with KEGG pathways. Deregulated pathways identified in both carcinoma and sarcoma include: cell cycle, transcriptional regulation, Ras and p53 signaling. Some additional pathways are putatively associated with sarcoma only, including MAPK and PI3K-Akt signaling. We report here the differences between sarcoma and carcinoma components of UCS from multiple molecular perspectives. From the genomic AI and DE analysis, the carcinoma aberrations appear to be mostly a subset of the sarcoma tumor profiles, where sarcoma samples appear to be more highly aberrant compared to the carcinoma samples. One possible inference from this is that the sarcoma originated and evolved from the carcinoma cells. Citation Format: Yihua Liu, Zachary Weber, F. Anthony San Lucas, Aditya Deshpande, Raed Sulaiman, Mary Fagerness, Natasha Flier, Joseph Sulaiman, Christel M. Davis, Jerry Fowler, Gareth E. Davies, David Starks, Luis Rojas-Espaillat, Paul Scheet, Erik A. Ehli. Tumor profiling of separated carcinomatous and sarcomatous components from uterine carcinosarcoma biopsies provides insights into their development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2463. doi:10.1158/1538-7445.AM2017-2463