Variants In Cancer-related Genes Research Articles

Impact of additional genetic abnormalities at diagnosis of chronic myeloid leukemia for first-line imatinib-treated patients receiving proactive treatment intervention.

The BCR::ABL1 gene fusion initiates chronic myeloid leukemia (CML); however, evidence has accumulated from studies of highly selected cohorts that variants in other cancer-related genes are associated with treatment failure. Nevertheless, the true incidence and impact of additional genetic abnormalities (AGA) at diagnosis of chronic phase (CP)-CML is unknown. We sought to determine whether AGA at diagnosis in a consecutive imatinib-treated cohort of 210 patients enrolled in the TIDEL-II trial influenced outcome despite a highly proactive treatment intervention strategy. Survival outcomes including overall survival, progression-free survival, failure-free survival, and BCR::ABL1 kinase domain mutation acquisition were evaluated. Molecular outcomes were measured at a central laboratory and included major molecular response (MMR, BCR::ABL1 ≤0.1%IS), MR4 (BCR::ABL1 ≤0.01%IS), and MR4.5 (BCR::ABL1 ≤0.0032%IS). AGA included variants in known cancer genes and novel rearrangements involving the formation of the Philadelphia chromosome. Clinical outcomes and molecular response were assessed based on the patient's genetic profile and other baseline factors. AGA were identified in 31% of patients. Potentially pathogenic variants in cancer-related genes were detected in 16% of patients at diagnosis (including gene fusions and deletions) and structural rearrangements involving the Philadelphia chromosome (Ph-associated rearrangements) were detected in 18%. Multivariable analysis demonstrated that the combined genetic abnormalities plus the EUTOS long-term survival clinical risk score were independent predictors of lower molecular response rates and higher treatment failure. Despite a highly proactive treatment intervention strategy, first-line imatinib-treated patients with AGA had poorer response rates. These data provide evidence for the incorporation of genomically-based risk assessment for CML.

Integrated genomic sequencing in myeloid blast crisis chronic myeloid leukemia (MBC-CML), identified potentially important findings in the context of leukemogenesis model

Chronic myeloid leukemia (CML) is a model of leukemogenesis in which the exact molecular mechanisms underlying blast crisis still remained unexplored. The current study identified multiple common and rare important findings in myeloid blast crisis CML (MBC-CML) using integrated genomic sequencing, covering all classes of genes implicated in the leukemogenesis model. Integrated genomic sequencing via Whole Exome Sequencing (WES), Chromosome-seq and RNA-sequencing were conducted on the peripheral blood samples of three CML patients in the myeloid blast crisis. An in-house filtering pipeline was applied to assess important variants in cancer-related genes. Standard variant interpretation guidelines were used for the interpretation of potentially important findings (PIFs) and potentially actionable findings (PAFs). Single nucleotide variation (SNV) and small InDel analysis by WES detected sixteen PIFs affecting all five known classes of leukemogenic genes in myeloid malignancies including signaling pathway components (ABL1, PIK3CB, PTPN11), transcription factors (GATA2, PHF6, IKZF1, WT1), epigenetic regulators (ASXL1), tumor suppressor and DNA repair genes (BRCA2, ATM, CHEK2) and components of spliceosome (PRPF8). These variants affect genes involved in leukemia stem cell proliferation, self-renewal, and differentiation. Both patients No.1 and No.2 had actionable known missense variants on ABL1 (p.Y272H, p.F359V) and frameshift variants on ASXL1 (p.A627Gfs*8, p.G646Wfs*12). The GATA2-L359S in patient No.1, PTPN11-G503V and IKZF1-R208Q variants in the patient No.3 were also PAFs. RNA-sequencing was used to confirm all of the identified variants. In the patient No. 3, chromosome sequencing revealed multiple pathogenic deletions in the short and long arms of chromosome 7, affecting at least three critical leukemogenic genes (IKZF1, EZH2, and CUX1). The large deletion discovered on the short arm of chromosome 17 in patient No. 2 resulted in the deletion of TP53 gene as well. Integrated genomic sequencing combined with RNA-sequencing can successfully discover and confirm a wide range of variants, from SNVs to CNVs. This strategy may be an effective method for identifying actionable findings and understanding the pathophysiological mechanisms underlying MBC-CML, as well as providing further insights into the genetic basis of MBC-CML and its management in the future.

Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products

BackgroundIndian natural products have been anecdotally used for cancer treatment but with limited efficacy. To better understand their mechanism, we examined the publicly available data for the activity of Indian natural products in the NCI-60 cell line panel.MethodsWe examined associations of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with in vitro response to treatment with 75 compounds derived from Indian plant-based natural products. We analyzed expression measures for annotated transcripts, lncRNAs, and miRNAs, and protein-changing single nucleotide variants in cancer-related genes. We also examined the similarities between cancer cell line response to Indian natural products and response to reference anti-tumor compounds recorded in a U.S. National Cancer Institute (NCI) Developmental Therapeutics Program database.ResultsHierarchical clustering based on cell line response measures identified clustering of Phyllanthus and cucurbitacin products with known anti-tumor agents with anti-mitotic mechanisms of action. Curcumin and curcuminoids mostly clustered together. We found associations of response to Indian natural products with expression of multiple genes, notably including SLC7A11 involved in solute transport and ATAD3A and ATAD3B encoding mitochondrial ATPase proteins, as well as significant associations with functional single nucleotide variants, including BRAF V600E.ConclusionThese findings suggest potential mechanisms of action and novel associations of in vitro response with gene expression and some cancer-related mutations that increase our understanding of these Indian natural products.

Abstract P3-07-01: Young women with breast cancer and high risk family history but no high penetrance germline mutations have a higher load of rare high functional impact germline variants in cancer relevant genes

Abstract Background: There is an incomplete understanding of why some women develop breast cancer 20-25 years earlier than the majority of women. Only 30-40% of women with high risk family history are found to have known cancer predisposing mutations. This phenomenon is referred to as “missing heredity”. We hypothesize that women with high-risk cancer family history but no known high penetrance cancer predisposing mutations who develop breast cancer at a young age have a higher deleterious load of germline high functional impact (gHFI) single nucleotide variants in cancer relevant genes. Methods: 94 women diagnosed with breast cancer age <50 with high risk cancer family history who tested negative for germline cancer predisposing mutations were identified at Yale Cancer Prevention Clinic (YCPC). 149 controls, healthy Caucasian individuals age > 65 with no cancer family history were identified from Yale Generations project. Whole-exome sequencing (WES) was performed on peripheral blood from 94 cases, 149 controls, and 42 matched tumors. WES data was analyzed from 1,112 female breast cancer cases with first-degree breast cancer family history and 50,887 healthy women without breast cancer family history from UKBiobank. Rare gHFI variants were defined as nonsynonymous variants predicted as deleterious in MetaSVM, or loss-of-function in gnormAD, or pathogenic in ClinVar database with mutation frequency <0.01. Hallmark genes were 1,558 genes involved in 21 cancer pathways and 83 cancer predisposition genes (CPGs). 468 somatic cancer genes were used. Rare gHFI in cases vs controls were compared using SNP-set (Sequence) Kernel Association Test (SKAT). Somatic mutations in YCPC vs 652 ER+ breast cancer TCGA cases were compared using 13/468 cancer genes mutated >5% of cases using Fisher’s exact test. FDRs were calculated using Benjamini & Hochberg. Results: The majority of YCPC patients were Caucasian (78.7%), median age (43.5), with invasive ductal carcinoma (85.1%), ER+PR+HER2- (67.0%). YCPC patients had a higher average burden of rare gHFI variants in cancer hallmark genes (excluding CPGs) compared to controls (p=0.0075, adjusted for race), but did not show a higher germline burden in CPGs. Similarly, UKBiobank breast cancer patients with a family history had a higher germline variant burden in hallmark genes (excluding CPGs) compared to controls (p=0.0368). The main pathways affected by gHFI in the YCPC cohort were adaptive immunity (p=1.61 x 10-8) and extracellular matrix (p=0.0034). Thirty six (87.8%) YCPC matched tumors carried somatic mutations in known cancer related genes. Compared to TCGA, YCPC samples had fewer TP53 mutations (5% vs 17%, FDR = 0.27), but more mutations in CHEK2, GNAQ, APC, and SDHA (FDR<0.028). Conclusions: Our cohort of young women with breast cancer and high risk family history with no known germline high penetrance cancer gene mutations showed a higher burden of germline high functional impact variants in hallmark cancer genes. This higher germline variant burden suggests that the totality of gHFI variants in cancer related genes could explain why these women develop breast cancer at a younger age. CohortRace (%)AgeCases (N)Control (N)GenesetAverage Case BurdenAverage Case BurdenSKAT testYaleCaucasian (78.7)439414983 CPGs0.27660.30200.56921508 Hallmark4.23404.18790.0075UK BiobankBritish (100)5611125088783 CPGs0.37410.28064.19x10-51508 Hallmark3.36423.33990.0368 Citation Format: Mariya Rozenblit, Tao Qing, Yixuan Ye, Hongyu Zhao, Erin Hofstatter, Vinit Singh, Emily Reisenbichler, Michael Murray, Lajos Pusztai. Young women with breast cancer and high risk family history but no high penetrance germline mutations have a higher load of rare high functional impact germline variants in cancer relevant genes [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-07-01.

Prevalence of cancer susceptibility variants in patients with multiple Lynch syndrome related cancers

Along with early-onset cancers, multiple primary cancers (MPCs) are likely resulting from increased genetic susceptibility; however, the associated predisposition genes or prevalence of the pathogenic variants genes in MPC patients are often unknown. We screened 71 patients with MPC of the stomach, colorectal, and endometrium, sequencing 65 cancer predisposition genes. A subset of 19 patients with early-onset MPC of stomach and colorectum were further evaluated for variants in cancer related genes using both normal and tumor whole exome sequencing. Among 71 patients with MPCs, variants classified to be pathogenic were observed in 15 (21.1%) patients and affected Lynch Syndrome (LS) genes: MLH1 (n = 10), MSH6 (n = 2), PMS2 (n = 2), and MSH2 (n = 1). All carriers had tumors with high microsatellite instability and 13 of them (86.7%) were early-onset, consistent with LS. In 19 patients with early-onset MPCs, loss of function (LoF) variants in RECQL5 were more prevalent in non-LS MPC than in matched sporadic cancer patients (OR = 31.6, 2.73–1700.6, p = 0.001). Additionally, there were high-confidence LoF variants at FANCG and CASP8 in two patients accompanied by somatic loss of heterozygosity in tumor, respectively. The results suggest that genetic screening should be considered for synchronous cancers and metachronous MPCs of the LS tumor spectrum, particularly in early-onset. Susceptibility variants in non-LS genes for MPC patients may exist, but evidence for their role is more elusive than for LS patients.

Frequency of pathogenic/likely pathogenic germline variants in cancer-related genes among children with acute leukemia in Saudi Arabia.

The frequency of pathogenic/likely pathogenic (P/LP) germline mutations in cancer-related genes among children with cancer in highly consanguineous populations is not well studied. Whole-exome sequencing of germline DNA was performed in 60 children with acute leukemia. We used the St. Jude Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE) data portal for the classification of germline variants by the St. Jude Medal Ceremony pipeline. Fifty-seven patients had acute lymphoblastic leukemia (ALL) and three patients had acute myeloid leukemia. Parental consanguinity was present in 27 (45%) patients. All patients were of Arab ancestry. Three patients (5%) had a history of cancer in their siblings. Five patients (8.3%) had P/LP germline mutations in cancer-related genes. Three patients with B-ALL had heterozygous pathogenic mutations in TP53, BRCA1, and BRCA2; one patient with B-ALL had homozygous pathogenic mutation in PMS2; and one patient with T-ALL had LP homozygous mutation in AK2 that was associated with reticular dysgenesis. Among patients who had history of parental consanguinity, three (11%) had P/LP germline mutations compared with two (8%) in the absence of parental consanguinity. Fourteen (23%) patients had gold medal variants in cancer-related genes, 13 were heterozygous, and one was homozygous. Silver medal variants were present in 35 (58%) patients; all were heterozygous except one homozygous. Children with acute leukemia in Saudi Arabia had low frequency of P/LP mutations in cancer-related genes despite the high rate of consanguinity. Larger studies using whole-genome sequencing are needed to further explore the heritability of childhood leukemia.

Abstract P5-03-04: Co-segregation of rare possibly-damaging variants in cancer-related genes correlates with phenotypic homogeneity in familial breast cancer

Abstract BACKGROUND Breast cancer (BC) is a complex disease. While Mendelian mutations in high-penetrance genes predispose to some familial forms, others are due to multiple common low-penetrance polymorphisms. However, it is unclear if the combination of some rare coding variants has an effect. As some Mendelian forms demonstrate genotype-phenotype correlations, we hypothesized co-segregation of rare variants in cancer-related genes would be more frequent in high-risk families with a uniform BC phenotype among relatives. METHODS Whole-exome sequencing was performed on germline DNA from unrelated BC patients referred for genetic testing but without a causative mutation and for which DNA was available from at least one second relative with BC. We retained rare (< 1.5% in ExaC) in silico possibly damaging variants (splice alteration, nonsense or frameshift mutation, or missense variant considered deleterious by at least 2 different algorithms) in a list of 735 cancer or DNA repair related genes. We assessed correlation between segregation of these variants in affected relatives (studied by Sanger sequencing) and tumor phenotypes. A familial uniform BC phenotype was denoted as sharing the same BC histology and the same clinical molecular classification, based on the expression of the hormone receptors and HER2. RESULTS Of the 54 families, 23 (43%) presented a uniform phenotype across the affected relatives. We identified 251 variants. The mean number of variants tested did not differ between families with a similar BC phenotype and families with different BC phenotypes (4.3 vs 4.9 respectively, two-sided T-test p=0.19). The proportion of disease co-segregating variants inside each family was however significantly higher in families with a uniform BC phenotype than in families with a heterogeneous BC phenotype (57.8% vs 30.2%, p<0.01 adjusted for the number of relatives and meioses within each family). Sequencing of matched tumor DNA, obtained for 44 probands, revealed co-segregating variants were more frequently enriched by a somatic event (18.6 vs 4.5%, Mann-Whitney test p=0.042 and 8.3 vs 1.1%, p=0.031 for the families with a uniform or a heterogeneous breast cancer phenotype, respectively). CONCLUSION In this cohort of families at high risk of BC, the proportion of co-segregating variants was significantly higher in the families in which the affected relatives shared a uniform BC phenotype. Investigation of oligogenic models could be more pertinent in this subgroup of families. The theory of bi-allelic gene inactivation required to drive cancer, shown for several Mendelian genes, could also be pertinent in the oligogenic model of inheritance. This study should be replicated in an independent cohort for confirmation. Citation Format: Cedric Van Marcke, Raphaël Helaers, Céline A Schoonjans, Jérôme Ambroise, Martine Berlière, Jean-Luc Canon, Peter Vuylsteke, Jean-Pascal Machiels, Miikka Vikkula, Francois P Duhoux. Co-segregation of rare possibly-damaging variants in cancer-related genes correlates with phenotypic homogeneity in familial breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-03-04.

BCR-ABL1 and beyond

Chronic myeloid leukaemia (CML) is characterised by the BCR-ABL1 fusion, which causes activated and abnormal cell signalling. If untreated, CML progresses to a rapidly fatal acute leukaemia at a median of 3 years. BCR-ABL1 can be superbly targeted by tyrosine kinase inhibitor drugs and most patients now have a life expectancy approaching that of the general population. However, about 20% of patients fail therapy and require a rapid change of treatment to avoid the risk of disease progression and death. Molecular monitoring of BCR-ABL1 transcript levels using quantitative PCR is now the recommended monitoring strategy and can detect treatment failure and emerging drug resistance. Acquired resistance is most frequently associated with mutations in the BCR-ABL1 kinase domain that interfere with drug binding. These are detected in ∼50% of resistant patients, but the other resistance mechanisms are not well understood. Data is emerging from next-generation sequencing studies that somatic variants in cancer-related genes occur at a high frequency at drug resistance. Furthermore, these mutations have also been detected in some patients at diagnosis and are associated with a poor outcome. Next-generation sequencing may provide important prognostic information for CML patients at diagnosis and resistance and identify targets for therapy.

Prospective Study of Cancer Genetic Variants: Variation in Rate of Reclassification by Ancestry.

In germline genetic testing, variants from understudied ancestries have been disproportionately classified as being of uncertain significance. We hypothesized that the rate of variant reclassification likewise differs by ancestry. Nonbenign variants in actionable genes were collected from consenting subjects undergoing genetic testing at two Southern California sites from September 1996 through December 2016. Variant reclassifications were recorded as they were received, until February 2017 or reclassification to benign. Excluding duplicate variants (same ancestry, laboratory, classification), generalized linear models for the hereditary breast cancer genes (BRCA1/2) and other variants investigated whether rate of reclassification differed for seven categories of ancestry compared with non-Hispanic European. Models took into account laboratory, year, gene, sex, and current classification (handled as a time-dependent covariate) and were adjusted for multiple hypothesis testing. Among 1483 nonbenign variants, 693 (46.7%) involved BRCA1/2. Overall, 268 (18.1%) variants were reclassified at least once. Few (9.7%) reclassified variants underwent a net upgrade in pathogenicity. For BRCA1/2 variants, reclassification rates varied by ancestry and increased over time, more steeply for ancestries with lower initial rates (African, Ashkenazi, Chinese) than for ancestries whose initial rates were high (Middle Eastern) or similar to non-Hispanic European (non-Chinese Asian, Native American, Hispanic). In contrast, reclassification rates of non-BRCA1/2 variants did not vary over time but were elevated for most minority ancestries except non-Chinese Asian and Native American. For nonbenign variants in cancer-related genes, the rates at which reclassifications are issued vary by ancestry in ways that differ between BRCA1/2 and other genes.

Breast cancer risk and germline genomic profiling of women with neurofibromatosis type 1 who developed breast cancer.

NF1 mutations predispose to neurofibromatosis type 1 (NF1) and women with NF1 have a moderately elevated risk for breast cancer, especially under age 50. Germline genomic analysis may better define the risk so screening and prevention can be applied to the individuals who benefit the most. Survey conducted in several neurofibromatosis clinics in the United States has demonstrated a 17.2% lifetime risk of breast cancer in women affected with NF1. Cumulated risk to age 50 is estimated to be 9.27%. For genomic profiling, fourteen women with NF1 and a history of breast cancer were recruited and underwent whole exome sequencing (WES), targeted genomic DNA based and RNA-based analysis of the NF1 gene. Deleterious NF1 pathogenic variants were identified in each woman. Frameshift mutations because of deletion/duplication/complex rearrangement were found in 50% (7/14) of the cases, nonsense mutations in 21% (3/14), in-frame splice mutations in 21% (3/14), and one case of missense mutation (7%, 1/14). No deleterious mutation was found in the following high/moderate-penetrance breast cancer genes: ATM, BRCA1, BRCA2, BARD1, BRIP1, CDH1, CHEK2, FANCC, MRE11A, NBN, PALB2, PTEN, RAD50, RAD51C, TP53, and STK11. Twenty-five rare or common variants in cancer related genes were discovered and may have contributed to the breast cancers in these individuals. Breast cancer predisposition modifiers in women with NF1 may involve a great variety of molecular and cellular functions.

Abstract 516: High-throughput functional evaluation of variants of unknown significance in EGFR

Abstract Since transforming mutations in epidermal growth factor receptor gene (EGFR) were first identified in non-small-cell lung carcinoma (NSCLC), advancement of diagnostics for such mutations, and evolution of targeted therapeutics against EGFR has driven unprecedented improvements in the management as well as outcome of patients with this lethal disease. However, next-generation sequencer (NGS)-driven extensive analyses on NSCLC have revealed a large number of variants of uncertain significance (VUS) in EGFR and other regions in the cancer genome that await further investigation. Here we present a mixed all nominated mutants in one (MANO) method to evaluate the transforming potential and drug sensitivity of VUS of oncogenes, and applied this method to 101 non-synonymous EGFR mutants in a high-throughput manner. The sensitivity of individual mutants to tyrosine kinase inhibitors (TKIs) against EGFR was shown diverged, ranging from relatively insensitive mutations such as missense mutations within exon 19 to a highly resistant mutation within exon 21. Our data thus support the importance of examining uncommon mutations within EGFR, and also of functional evaluation of such mutations. Our MANO method may become a novel foundation for in vitro and in vivo assessments of variants of cancer-related genes to deliver precision medicine to individual cancer patients. Citation Format: Shinji Kohsaka, Masaaki Nagano, Toshihide Ueno, Yoshiyuki Suehara, Takuo Hayashi, Naoko Shimada, Kazuhisa Takahashi, Kenji Suzuki, Kazuya Takamochi, Fumiyuki Takahashi, Hiroyuki Mano. High-throughput functional evaluation of variants of unknown significance in EGFR [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 516. doi:10.1158/1538-7445.AM2017-516

Clinical Exome Sequencing Unravels New Disease Causing Mutations in Myeloproliferative Neoplasms (MPNs): A Pilot Study in Patients from the State of Qatar

In Qatar, a cluster of ET familial cases (25 families from 5 major tribes) has been documented. This observation represents a unique interest for the scientific community worldwide, as the cultural traditions of tribal marriages between 1stcousins is expected to lead to the preservation of a limited genetic pool (giving rise to founder effects). CES was employed to analyze a 3 probands from three unrelated families (S1, S2, S3). All 6 patients were Qatari belonging to consanguineous families with a positive family history of MPNs. CES confirmed the diagnosis in the 3 probands: two patients (S1 and S2) were classified as Essential Thrombocythemia (ET), one patient (S3) as unclassified MPNs. In the other 3 subjects (S4, S4, S6), several shared deleterious mutations and polymorphisms were uncovered. CES identified 10 novel mutations in known genes as well as 7 novel candidate genes and 2 (6%) previously reported mutations in the three probands (S1, S2, S3) who's diagnosis was confirmed . S1: a confirmed diagnosis and phenotype of ET (JAK2 and THPO), S2: a confirmed diagnosis and phenotype of ET (JAK2 and MPL) and S3: a confirmed diagnosis of U-MPNs (TERT, ATM, NUMA1 and ASXL) The mutations/variants were classified according to ACMG recommendations into 5 classes. The number of mutations/variants detected in each class is as follows: Class 1 - Previously reported as disease-causing: 6 Class 2 - Previously unreported, but of the type which can cause the disorder: 3 Class 3 - Previously unreported, may or may not be the cause of the disorder (Variant of uncertain clinical significance): 48 Class 4 - Previously unreported but likely neutral: 1 Class 5 - Previously reported as neutral: 3 CES identified a total of 61 interesting variants which occurred in 50 genes, 13 were recurrently. The vast majority of the prioritized variants were missense 50(82%); the remaining were frameshift (small insertions and deletions) 10(16%) or affecting splicing sites 1(2%). The most interesting finding is the presence of 10 novel mutations in known genes related to MPNs as well as 7 variants in novel candidate genes in the three probands who's diagnosis was confirmed via CES. This study presents novel data that contributes to understanding the high level of genetic complexity in MPNs Qatari patients. It has identified new variants in cancer-related genes potentially involved in the pathogenesis of the disease Our study of familial MPNs led to the identification of new disease-causing mutations and variants, some previously described as either germline or somatic. A clinical cohort of 3 Qatari probands suspected to have MPNs as well as three family members with a positive family history of MPNs presented at National Center for Cancer Care (NCCCR) S1) is a female who presented with high hemoglobin (Hb) level, red blood cells (RBCs) count, leukocytosis with neutrophilia, very high platelets and normal erythropoietin (EPO); subject 2 (S2) is a female who presented with normal Hb, RBCs count, slightly high WBCs and high platelets; subject 3 (S3) is a male who presented with high Hb, normal WBCs and EPO 3 family members, subject 4 -a mother presented with normal Hb level, sustained high RBCs count and slightly high WBCs count, subject 5 a daughter presented with unexplained sustained erythrocytosis, leukocytosis (absolute neutrophilia, for more than 2 years Chronic headache, normal MRI brain and no progression to cancer no Ischemic events, subject 6- healthy daughter with normal CBC indicesThe pattern of mutations identified was unique. In this study 10 novel mutations in known genes already implicated in the pathogenesis of MPNs were detected including THPO, CBL, ASXL1, MPL (2x), BCL2, MYO18B, MTOR, PDGFRB, TERT. Mutations/variants were detected in 9 genes not previously associated with MPNs suggesting potential novel gene associations. Pathogenic/likely pathogenic mutations, uncertain variants and neutral/likely neutral variants were identified using the CES approach. A complex combination of mutations was observed in our cohort of subjects. For example in subject 1 (S1), an ET patient, the following mutations were observed: THPO S184R, ITGA2 R76Q, JAK2 V617F, CBL E196G, CBFB G180S, FANCA S858R, ASXL1 T600P fs103. The following detailed analysis of each mutation reveals that all these mutations could potentially play a role in the pathogenesis of MPNs Disclosures No relevant conflicts of interest to declare.

Frequent variations in cancer-related genes may play prognostic role in treatment of patients with chronic myeloid leukemia.

BackgroundGenome variability of host genome and cancer cells play critical role in diversity of response to existing therapies and overall success in treating oncological diseases. In chronic myeloid leukemia targeted therapy with tyrosine kinase inhibitors demonstrates high efficacy in most of the patients. However about 15 % of patients demonstrate primary resistance to standard therapy. Whole exome sequencing is a good tool for unbiased search of genetic variations important for prognosis of survival and therapy efficacy in many cancers. We apply this approach to CML patients with optimal response and failure of tyrosine kinase therapy.ResultsWe analyzed exome variations between optimal responders and failures and found 7 variants in cancer-related genes with different genotypes in two groups of patients. Five of them were found in optimal responders: rs11579366, rs1990236, rs176037, rs10653661, rs3803264 and two in failures: rs3099950, rs9471966. These variants were found in genes associated with cancers (ANKRD35, DNAH9, MAGEC1, TOX3) or participating in cancer-related signaling pathways (THSD1, MORN2, PTCRA).ConclusionWe found gene variants which may become early predictors of the therapy outcome and allow development of new early prognostic tests for estimation of therapy efficacy in CML patients. Normal genetic variation may influence therapy efficacy during targeted treatment of cancers.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0308-7) contains supplementary material, which is available to authorized users.

Comparison of Genetic Variants in Cancer-Related Genes between Chinese Hui and Han Populations

BackgroundThe Chinese Hui population, as the second largest minority ethnic group in China, may have a different genetic background from Han people because of its unique demographic history. In this study, we aimed to identify genetic differences between Han and Hui Chinese from the Ningxia region of China by comparing eighteen single nucleotide polymorphisms in cancer-related genes.MethodsDNA samples were collected from 99 Hui and 145 Han people from the Ningxia Hui Autonomous Region in China, and SNPs were detected using an improved multiplex ligase detection reaction method. Genotyping data from six 1000 Genomes Project population samples (99 Utah residents with northern and western European ancestry (CEU), 107 Toscani in Italy (TSI), 108 Yoruba in Ibadan (YRI), 61 of African ancestry in the southwestern US (ASW), 103 Han Chinese in Beijing (CHB), and 104 Japanese in Tokyo (JPT)) were also included in this study. Differences in the distribution of alleles among the populations were assessed using χ2 tests, and FST was used to measure the degree of population differentiation.ResultsWe found that the genetic diversity of many SNPs in cancer-related genes in the Hui Chinese in Ningxia was different from that in the Han Chinese in Ningxia. For example, the allele frequencies of four SNPs (rs13361707, rs2274223, rs465498, and rs753955) showed different genetic distributions (p<0.05) between Chinese Ningxia Han and Chinese Ningxia Hui. Five SNPs (rs730506, rs13361707, rs2274223, rs465498 and rs753955) had different FST values (FST >0.000) between the Hui and Han populations.ConclusionsThese results suggest that some SNPs associated with cancer-related genes vary among different Chinese ethnic groups. We suggest that population differences should be carefully considered in evaluating cancer risk and prognosis as well as the efficacy of cancer therapy.

Abstract 4808: Identification of genes with variants in HPV-associated head and neck squamous cell carcinoma

Abstract Introduction: Human papilloma virus (HPV)-associated head and neck squamous cell carcinomas have a distinct etiologic mechanism of carcinogenesis compared to non-HPV associated HNSCCs. These tumors are also generally thought to harbor less mutations compared to non-HPV associated HNSCCs. However, recent research suggests that not only do HPV-associated HNSCCs contain mutations, they are distinct from mutations found in non-HPV associated HNSCCs. Identification of these genetic variants is necessary to determine potential prognostic markers or novel insight into the mechanism of HPV-induced carcinogenesis. In this study, we identified genes with variants that are more common in HPV-associated HNSCCs compared to non-HPV associated HNSCCs. Materials and methods: Thirty-six primary head and neck SCC (HNSCC) tumor samples were collected between 2011-2013 at University of Michigan hospital, of which 18 were determined to be HPV+ (type16, 18 or 35). Paired-end RNA-Seq libraries were generated using Illumina HiSeq for all samples and aligned to both the human and HPV genome. Variant calling was employed using an established pipeline to identify single nucleotide polymorphisms (SNPs) from RNA-Seq data. Briefly, data was aligned using STAR, followed by indel realignment and base recalibration. Variants were called using HaplotypeCaller and filtered by Fisher Strand values (FS &amp;gt; 30.0) and Qual By Depth values (QD &amp;lt; 2.0). Variants were annotated and filtered by SnpEff and SnpSift to determine genes with nonsynonymous variants by HPV status. Results: Out of all samples, nine genes showed nonsynonymous variants in HPV-associated tumors greater than 60% of the time compared to non-HPV associated tumors. These are PTCH1 (associated with eosophageal squamous cell carcinoma), ATRX (involved in chromatin binding), ERCC2 (associated with skin cancers), FOXA1 (transcription factor), CCDC6 (associated with thyroid papillary carcinoma), FNBP1 (involved in lipid binding), and POU5F1 (transcription factor). Seventy-five percent of the samples with nonsynonymous variants in TMPRSS2, a gene shown to be associated with prostate cancer, were HPV-associated tumors. Eighty-two percent of all samples with nonsynonymous variants in FANCD2, a gene involved in maintenance of chromosomal stability, were HPV-associated tumors. Conclusion: Although HPV-associated HNSCCs generally harbor fewer mutations than non-HPV associated HNSCCs, our data suggests they do contain variants in cancer-related genes. This is important as these genes may play a role in the mechanism of HPV-induced tumorigenesis subsequent to viral initiation. Citation Format: Shama Virani, Pelle B. Hall, Yanxiao Zhang, Lada A. Koneva, Alisha Virani, Katie M. Rentschler, Thomas E. Carey, Laura S. Rozek, Maureen A. Sartor. Identification of genes with variants in HPV-associated head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4808. doi:10.1158/1538-7445.AM2015-4808

Abstract 2745: Exome sequencing analysis of 41 patients with Familial Colorectal Cancer Type X (FCCTX)

Abstract Colorectal cancer (CRC) is the second most common cancer. About 10% of CRC are hereditary including familial adenomatous polyposis (FAP), hereditary non-polyposis colorectal cancer (HNPCC), and rare syndromes. While genetics of FAP and rare syndromes is well studied (APC, STK11, AXIN2), only ∼40-50% of HNPCC have identifiable DNA mismatch-repair gene defects. CRC cases fulfilling Amsterdam Criteria I for HNPCC with normal DNA mismatch repair and elevated risk of microsatellite-stable CRC are called Familial Colorectal Cancer Type X (FCCTX). Compared to HNPCC, FCCTX patients are older, with left-sided CRC, and frequent polyps. We hypothesize that FCCTX is a dominant Mendelian cancer syndrome with incomplete penetrance caused by rare, family-specific mutations in oncogenes and tumor suppressors. To identify novel mutations and genes involved in FCCTX, we performed germline exome sequencing of microsatellite-stable familial CRC from Molecular Epidemiology of Colorectal Cancer (MECC) study, a population-based, case-control CRC study in Northern Israel. We selected 41 patients from 38 FCCTX families with extensive family history of microsatellite stable (MSS) or microsatellite instable low (MSI-Low) CRC. Patients were Ashkenazi Jewish, Sephardi Jewish, Europeans, Druze, and Arabs. Similar to previous studies, stomach cancer was second most common in the families, and left-sided CRC was more prevalent. Exome sequencing of all patients generated 52,722 variants. Stepwise filtering analysis was applied to identify candidate variants and genes. We selected all novel and rare (minor allele frequency &amp;lt;0.001) functional variants in cancer-related genes from literature and cancer databases (COSMIC and TCGA). In line with dominant inheritance, only heterozygous variants predicted to be deleterious by multiple bioinformatic tools were selected. We identified 627 variants in 387 genes. Gene enrichment analysis showed regulation of apoptosis and cell cycle, DNA repair, cell adhesion, and cell surface receptor linked signal transduction. As expected, we found APC*I1307K founder mutation in three Ashkenazi Jewish patients, one novel APC mutation (p.1289_1291del) in a non-Jewish European patient, and found a mutation in MSH6. We identified three promising candidate genes and performed segregation analysis in families. Our preliminary data suggest several novel candidate genes for FCCTX, although older age at onset and incomplete penetrance complicate the interpretation of the results. Further population-based and family-based studies are being conducted to confirm our findings. Citation Format: Marilena Melas, Hung N. Luu, Gad Rennert, Flavio Lejbkowicz, Stephen B. Gruber, Georgia L. Wiesner, Leon Raskin. Exome sequencing analysis of 41 patients with Familial Colorectal Cancer Type X (FCCTX). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2745. doi:10.1158/1538-7445.AM2015-2745

Novel Insights into Breast Cancer Genetic Variance through RNA Sequencing

Using RNA sequencing of triple-negative breast cancer (TNBC), non-TBNC and HER2-positive breast cancer sub-types, here we report novel expressed variants, allelic prevalence and abundance, and coexpression with other variation, and splicing signatures. To reveal the most prevalent variant alleles, we overlaid our findings with cancer- and population-based datasets and validated a subset of novel variants of cancer-related genes: ESRP2, GBP1, TPP1, MAD2L1BP, GLUD2 and SLC30A8. As a proof-of-principle, we demonstrated that a rare substitution in the splicing coordinator ESRP2 (R353Q) impairs its ability to bind to its substrate FGFR2 pre-mRNA. In addition, we describe novel SNPs and INDELs in cancer relevant genes with no prior reported association of point mutations with cancer, such as MTAP and MAGED1. For the first time, this study illustrates the power of RNA-sequencing in revealing the variation landscape of breast transcriptome and exemplifies analytical strategies to search regulatory interactions among cancer relevant molecules.

The mannose-binding lectin (MBL2) haplotype and breast cancer: an association study in African-American and Caucasian women

Common genetic variants in cancer-related genes contribute to breast cancer. The innate immune system plays a crucial role in the immune surveillance against malignancies, thus it is plausible that genetic variations in key genes of the innate immunity such as the mannose-binding lectin (MBL), MBL2, could influence the risk for breast cancer. We investigated the association of MBL2 genotypes with breast cancer and conducted a comprehensive genotype and haplotype analysis of 26 MBL2 single nucleotide polymorphisms (SNPs) in a case-control study of breast cancer [166 African-American (AA) case patients versus 180 controls and 127 Caucasian (CAU) case patients versus 137 controls]. We observed that the A allele of the 3'-UTR SNP Ex4-1067 (NCBI SNP ID: rs10824792) was significantly associated with a decreased disease risk in AA women [odds ratio (OR) = 0.47, 95% confidence interval (CI) = 0.27-0.81]. Haplotype analysis of MBL2 showed that the frequency of the corresponding 3' haplotype TATAAC (Ex4-1483, Ex4-1067, Ex4-1047, Ex4-901, Ex4-710, 3238bp 3' STP) was lower in cases than controls among AA women (0.15 versus 0.21; P = 0.02) suggesting a protective effect after adjusting for covariates (OR = 0.51, 95% CI = 0.29-0.88, P = 0.018). In conclusion, this study presents preliminary evidence that common genetic variants in the 3'-UTR of MBL2 might influence the risk for breast cancer in AA women, probably in interaction with the 5' secretor haplotypes that are associated with high concentrations of MBL.