Constitutional DNA Samples Research Articles

ART-DeCo: easy tool for detection and characterization of cross-contamination of DNA samples in diagnostic next-generation sequencing analysis.

Next-generation sequencing (NGS) is routinely used for constitutional genetic analysis. However, cross-contamination between samples constitutes a major risk that could impact the results of the analysis. We have developed ART-DeCo, a tool using the allelic ratio (AR) of the Single Nucleotide Polymorphisms sequenced with regions of interest. When a sample is contaminated by DNA with a different genotype, unexpected ARs are obtained, which are in turn used for detection of contamination with a screening test, followed by identification and quantification of the contaminant. Following optimization, ART-DeCo was applied to 2222 constitutional DNA samples. The screening test was positive for 191 samples. In 33 cases (contamination percentages: 1.3% to 29.2%), the contaminant was identified and was mostly located in adjacent wells. Three other positive cases were due to barcoding errors or mixture of two DNA samples. Interestingly, the last contaminated sample corresponded to a bone marrow transplant recipient. Lastly, no contaminant was identified in 154 weakly positive ( < 4%) samples that were considered to be irrelevant to constitutional genetic analysis. ART-DeCo lends itself to mandatory quality control procedures, also highlighting the delicate steps of library preparation, resulting in practice improvement. Importantly, ART-DeCo can be implemented in any NGS workflow, from gene panel to genome-wide analyses. https://sourceforge.net/projects/ngs-art-deco/ .

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma

Recent genomic studies of sporadic clear cell renal cell carcinoma (ccRCC) have uncovered novel driver genes and pathways. Given the unequal incidence rates among men and women (male:female incidence ratio approaches 2:1), we compared the genome-wide distribution of the chromosomal abnormalities in both sexes. We observed a higher frequency for the somatic recurrent chromosomal copy number variations (CNVs) of autosomes in male subjects, whereas somatic loss of chromosome X was detected exclusively in female patients (17.1%). Furthermore, somatic loss of chromosome Y (LOY) was detected in about 40% of male subjects, while mosaic LOY was detected in DNA isolated from peripheral blood in 9.6% of them, and was the only recurrent CNV in constitutional DNA samples. LOY in constitutional DNA, but not in tumor DNA was associated with older age. Amongst Y-linked genes that were downregulated due to LOY, KDM5D and KDM6C epigenetic modifiers have functionally-similar X-linked homologs whose deficiency is involved in ccRCC progression. Our findings establish somatic LOY as a highly recurrent genetic defect in ccRCC that leads to downregulation of hitherto unsuspected epigenetic factors, and suggest that different mechanisms may underlie the somatic and mosaic LOY observed in tumors and peripheral blood, respectively.

Prognostic Implication of Somatic Mutations by Next Generation Sequencing: an Analysis from the MMRF CoMMpass Study in Newly Diagnosed Multiple Myeloma Patients

Introduction : High throughput techniques, such as massively parallel sequencing, are becoming an attractive approach to characterize multiple myeloma (MM) genomic profiles. However, the clinical relevance and contribution to risk assessment of such approaches need to be established. The Multiple Myeloma Research Foundation (MMRF)CoMMpass trial ([NCT01454297][1]) has collected data from 1000 newly-diagnosed MM patients enrolled worldwide and observed through an expected follow-up of up to eight-years. Comprehensive analysis of somatic mutations detected in purified MM cells could reveal disease features with prognostic value, which may not have been detected using traditional approaches. Materials and methods : We analyzed data from the interim analysis 8 cohort. CD138+ purified MM specimens from bone marrow aspirates and mononuclear cells from peripheral blood were collected at diagnosis. Whole exome libraries from both tumor and constitutional DNA samples were created. Somatic single nucleotide variants (SNV) were identified using three different variant callers (Seurat,Strelka andMutect), only nonsynonymous SNV calls made from at least two callers were included in the analysis. Patients were analyzed on an intention-to-treat basis. We evaluated the impact on progression free survival (PFS) of recurrently mutated genes (with at least a nonsynonymous SNV in more than 10 patients) in a Cox model adjusted for international staging system (ISS) and cytogenetic profile (high risk, standard risk and missing). An additive score related to mutated genes was calculated on the basis the level of each coefficient estimated using a Cox Model with backward selection based on theAkaikeInformation Criterion (AIC). Results: 517 patients with baseline somatic mutation data were included in the analysis. Median age at diagnosis was 64 years (range 27-93). All patients received novel agents as first line treatment; 236 (45.6%) received autologous stem cell transplantation (ASCT). Each patient showed a median number of 55 nonsynonymous somatic SNV (range 8-1970) in a median number of 47 genes (range 5-1741). Excluding immunoglobulin genes, the most recurrent mutated genes were KRAS (25%), NRAS (19.5%), TTN (12.1%), MUC16 (9.1%) and DIS3 (9.1%). Based on the results of a multivariable Cox model corrected for ISS and cytogeneticprofile, we created a scoring system determined by the mutational status of 9 genes identified in a nonbiased manner (Table 1). Three groups were identified: group I (score 0-2, 17%); group II (score=3, 51%), and group III (score >3, 32%). After a median follow-up of 371 days, the 18-month PFS rate was 93% for group I, 85% for group II, and 67% for group III. In a Cox model adjusted for ISS and cytogeneticprofile, the hazard ratio was 2.34 (p=0.112) for group II versus group I, and 5.96 (p<0.001) for group III versus I. The prognostic trend of the score was confirmed in different patient subgroups including ASCT/no ASCT, standard/high risk cytogenetic profile, ISS I, II, or III. Of note, 23.3% of patients in group I had an ISS III and 30.4% of patients in group III had an ISS I. Conclusion: The use of a prognostic model based on the mutational status of 9 recurrently mutated genes could improve risk assessment of newly-diagnosed MM patients. To our knowledge, this is the largest study correlating nonsynonymous somatic SNV with MM patients' outcome. Longer follow-up and validation in independent cohorts are needed to confirm our findings. ![Figure][2] ![Figure][2] Disclosures Larocca: Amgen, Celgene, BMS, Janssen-Cilag: Honoraria. Gay: Amgen: Honoraria; Bristol-Myers Squibb: Honoraria; Celgene: Honoraria; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Mundipharma: Membership on an entity's Board of Directors or advisory committees. Palumbo: Janssen Cilag: Honoraria; Takeda: Employment, Honoraria. [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01454297&atom=%2Fbloodjournal%2F128%2F22%2F2079.atom [2]: pending:yes

Prognostic Implication of Somatic Mutations By Next Generation Sequencing: An Analysis from the Mmrf Commpass Study in Newly Diagnosed Multiple Myeloma Patients

Introduction: High throughput techniques, such as massively parallel sequencing, are becoming an attractive approach to characterize multiple myeloma (MM) genomic profiles. However, the clinical relevance and contribution to risk assessment of such approaches need to be established. The Multiple Myeloma Research Foundation (MMRF)CoMMpass trial (NCT01454297) has collected data from 1000 newly-diagnosed MM patients enrolled worldwide and observed through an expected follow-up of up to eight-years. Comprehensive analysis of somatic mutations detected in purified MM cells could reveal disease features with prognostic value, which may not have been detected using traditional approaches.Materials and methods: We analyzed data from the interim analysis 8 cohort. CD138+ purified MM specimens from bone marrow aspirates and mononuclear cells from peripheral blood were collected at diagnosis. Whole exome libraries from both tumor and constitutional DNA samples were created. Somatic single nucleotide variants (SNV) were identified using three different variant callers (Seurat,Strelka andMutect), only nonsynonymous SNV calls made from at least two callers were included in the analysis.Patients were analyzed on an intention-to-treat basis. We evaluated the impact on progression free survival (PFS) of recurrently mutated genes (with at least a nonsynonymous SNV in more than 10 patients) in a Cox model adjusted for international staging system (ISS) and cytogenetic profile (high risk, standard risk and missing). An additive score related to mutated genes was calculated on the basis the level of each coefficient estimated using a Cox Model with backward selection based on theAkaikeInformation Criterion (AIC).Results: 517 patients with baseline somatic mutation data were included in the analysis. Median age at diagnosis was 64 years (range 27-93). All patients received novel agents as first line treatment; 236 (45.6%) received autologous stem cell transplantation (ASCT). Each patient showed a median number of 55 nonsynonymous somatic SNV (range 8-1970) in a median number of 47 genes (range 5-1741). Excluding immunoglobulin genes, the most recurrent mutated genes were KRAS (25%), NRAS (19.5%), TTN (12.1%), MUC16 (9.1%) and DIS3 (9.1%). Based on the results of a multivariable Cox model corrected for ISS and cytogeneticprofile, we created a scoring system determined by the mutational status of 9 genes identified in a nonbiased manner (Table 1). Three groups were identified: group I (score 0-2, 17%); group II (score=3, 51%), and group III (score >3, 32%). After a median follow-up of 371 days, the 18-month PFS rate was 93% for group I, 85% for group II, and 67% for group III. In a Cox model adjusted for ISS and cytogeneticprofile, the hazard ratio was 2.34 (p=0.112) for group II versus group I, and 5.96 (p<0.001) for group III versus I. The prognostic trend of the score was confirmed in different patient subgroups including ASCT/no ASCT, standard/high risk cytogenetic profile, ISS I, II, or III. Of note, 23.3% of patients in group I had an ISS III and 30.4% of patients in group III had an ISS I.Conclusion: The use of a prognostic model based on the mutational status of 9 recurrently mutated genes could improve risk assessment of newly-diagnosed MM patients. To our knowledge, this is the largest study correlating nonsynonymous somatic SNV with MM patients' outcome. Longer follow-up and validation in independent cohorts are needed to confirm our findings. [Display omitted] [Display omitted] DisclosuresLarocca:Amgen, Celgene, BMS, Janssen-Cilag: Honoraria. Gay:Amgen: Honoraria; Bristol-Myers Squibb: Honoraria; Celgene: Honoraria; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Mundipharma: Membership on an entity's Board of Directors or advisory committees. Palumbo:Janssen Cilag: Honoraria; Takeda: Employment, Honoraria.

Genomic analysis of cancer tissue reveals that somatic mutations commonly occur in a specific motif

Somatic mutations are hallmarks of cancer progression. We sequenced 26 matched human prostate tumor and constitutional DNA samples for somatic alterations in the SRD5A2, HPRT, and HSD3B2 genes, and identified 71 nucleotide substitutions. Of these substitutions, 79% (56/71) occur within a WKVnRRRnVWK sequence (a novel motif we call THEMIS [from the ancient Greek goddess of prophecy]: W=A/T, K=G/T, V=G/A/C, R=purine (A/G), and n=any nucleotide), with one mismatch allowed. Literature searches identified this motif with one mismatch allowed in 66% (37/56) of the somatic prostate cancer mutations and in 74% (90/122) of the somatic breast cancer mutations found in all human genes analyzed. We also found the THEMIS motif with one allowed mismatch in 88% (23/26) of the ras1 gene somatic mutations formed in the sensitive to skin carcinogenesis (SENCAR) mouse model, after induction of error-prone DNA repair following mutagenic treatment. The high prevalence of the motif in each of the above mentioned cases cannot be explained by chance (P<0.046). We further identified 27 somatic mutations in the error-prone DNA polymerase genes pol eta, pol kappa, and pol beta in these prostate cancer patients. The data suggest that most somatic nucleotide substitutions in human cancer may occur in sites that conform to the THEMIS motif. These mutations may be caused by "mutator" mutations in error-prone DNA polymerase genes.

TP53, BRCA1, and BRCA2 tumor suppressor genes are not commonly mutated in survivors of Hodgkin's disease with second primary neoplasms.

Despite recognition that second malignant neoplasms (SMNs) contribute significantly to mortality after the successful treatment of Hodgkin's disease (HD), little is known about the molecular events leading to secondary tumors. Factors contributing to second cancer risk include the carcinogenic effects of ionizing radiation and chemotherapy, in combination with possible host susceptibility. To clarify whether host genetic factors contribute to secondary tumorigenesis, we performed mutational analyses of the TP53, BRCA1, and BRCA2 tumor suppressor genes in a cohort of 44 HD patients developing one or more SMN. Family cancer histories and constitutional DNA samples were obtained from 44 HD patients with SMNs identified. Using DNA-based sequencing, we evaluated the TP53 gene in all 44 patients. Nineteen female patients developing one or more secondary breast cancer were also analyzed for mutations in the BRCA1 and BRCA2 breast cancer-susceptibility genes. Nineteen patients (43%) had more than one SMN, and 12 patients (27%) had a positive family history of cancer. One of 44 patients tested for TP53 harbored a novel homozygous germline abnormality. One of 19 patients tested for BRCA2 carried a previously described heterozygous inactivating mutation. We identified no germline BRCA1 mutations. Despite features suggestive of genetic predisposition, the TP53, BRCA1, and BRCA2 genes were not frequently mutated in this cohort of HD patients developing SMNs. Larger studies of these genes or investigations of other genes involved in cellular DNA damage response pathways may identify host genetic factors that contribute to secondary tumorigenesis.

Mutation analysis of the BRG1 gene in prostate cancer clinical samples

Previous studies in hereditary and sporadic prostate cancer have indicated the existence of a tumor suppressor gene in chromosomal region 19p13. The BRG1 gene in this region is one of the possible candidates, based on both the frequency of inactivating mutations in human cancer cell lines, including the prostate cancer cell line DU145, and its functional properties. To our knowledge, no studies have been done to evaluate possible involvement of the BRG1 gene in clinical prostate cancer. To accomplish this, we carried out a complete mutation analysis of all 35 BRG1 exons in tumor and constitutional DNA samples from 21 prostate cancer patients. We report the absence of somatic mutations in the panel of samples employed, but the existence of five germline single nucleotide polymorphisms (SNPs) in CpG islands of the BRG1 gene, among them, three novel ones. In conclusion, the study excludes the presence of common BRG1 mutations in prostate cancer.

Analysis of TP53 germline mutations in pediatric tumor patients using DNA microarray-based sequencing technology.

Whereas in sporadic human malignancies mutations of the TP53 tumor-suppressor gene occur in cancers of almost every organ and histologic subtype, patients with an inborn TP53 defect are at high risk to develop, in particular, soft tissue and bone sarcomas, brain tumors, leukaemias, adrenocortical tumors, and breast cancer. To demonstrate the usefulness of microarray technology applied to TP53 sequencing in pediatric tumors, we investigated young patients suffering from tumors typical of the Li-Fraumeni context who were, therefore, candidates for harboring inborn defects in tumor-suppressor genes. Six individuals were studied, including typical Li-Fraumeni patients as well as patients without any family history of cancer. DNA samples were independently analyzed for TP53 mutations by GeneChip and standard automated laser fluorescence (ALF) sequencing technology. The tumor and corresponding constitutional DNA samples clearly showed identical mutations which were confirmed by ALF sequencing. All coding exons (exons 2-11) of TP53 were analyzed simultaneously. The entire sequencing procedure and data analysis was carried out within 24 hr. The GeneChip TP53-sequencing assay may be feasible for routine molecular genetic diagnostics in determining the TP53 status of childhood-tumor patients and in enabling a disease management based on the genetic background of the individual.

Identification of MEN1 gene mutations in families with MEN 1 and related disorders.

Following identification of the MEN1 gene, we analysed patients from 12 MEN 1 families, 8 sporadic cases of MEN 1, and 13 patients with MEN 1-like symptoms (e.g. cases of familial isolated hyperparathyroidism (FIHPT), familial acromegaly, or atypical MEN 1 cases) for the presence of germline MEN1 mutations. The entire coding region of the MEN1 gene was sequenced, and mutations were detected in 11 MEN 1 families; one sporadic MEN 1 patient, one case of FIHPT and one MEN 1-like case. Constitutional DNA samples from individuals without MEN1 mutations were digested with several restriction enzymes, Southern blotted and probed with MEN1 cDNA to analyse for the presence of larger deletions of the MEN1 gene unable to be detected by PCR. One MEN 1 patient was found to carry such a deletion. This patient was heterozygous for the D418D polymorphism, however sequence analysis of RT-PCR products showed that only the variant allele was transcribed, thus confirming the result obtained by Southern analysis, which indicated loss of a region containing the initiation codon of one allele. © 2000 Cancer Research Campaign

Analysis of PTCH/SMO/SHH pathway genes in medulloblastoma.

Inactivation of the PTCH tumor suppressor gene occurs in a subset of sporadic medulloblastomas, suggesting that alterations in the PTCH pathway may be important in the development of this tumor. In order to address the frequency of genetic alterations affecting genes in this pathway, we used a combination of loss of heterozygosity (LOH) analysis, single-stranded conformational polymorphism (SSCP) analysis, and direct sequencing of DNA samples from sporadic primitive neuroectodermal tumors (PNETs). To identify alterations in the PTCH gene, we performed LOH analysis on 37 tumor DNA samples. Of those with matched constitutional DNA samples, one demonstrated LOH. Of those without matched constitutional DNA, six were homozygous with all markers. All exons of the PTCH gene were sequenced in these seven tumors, and three mutations were found. To identify alterations in the SHH and SMO genes, we analyzed all exons of both genes in 24 tumors with SSCP and sequenced any exons that showed aberrant band patterns. No mutations were found in either SHH or SMO in any tumor. We also identified the following genes as candidate tumor suppressors based on their roles in controlling hh/ptc signaling in Drosophila: EN-1 and EN-2, deletion of which results in a lack of cerebellar development in mice; SMAD family members 1-7, and protein kinase A subunits RIalpha, RIbeta, RIIbeta, Calpha, and Cbeta. Each of these genes was investigated in a panel of 24 matched constitutional and tumor DNA samples. Our search revealed no mutations in any of these genes. Thus, PTCH is the only gene in this complex pathway that is mutated with notable frequency in PNET. Genes Chromosomes Cancer 27:44-51, 2000.

A genetic model of melanoma tumorigenesis based on allelic losses

Previous karyotypic studies have indicated a possible series of non-random chromosomal events involved in progression of melanoma. We sought to verify and augment this model of melanocyte tumorigenesis by studying allelic deletions of markers mapping to these regions in 30 matched pairs of melanoma and constitutional DNA samples. Polymorphic loci on chromosomes 1, 7, 10, 11, 17, and 21 were analyzed and data combined with those previously obtained for chromosome arms 6q and 9p in the same series of tumours. The most frequent and earliest deletions were found on 9p (57%) and 10q (32%). With the exception of one case, no sample had loss of markers on another chromosome without concomitant loss of markers on 9p or 10q. Losses on 6q were also a frequent (31%) and early event whereas losses of loci on distal 1p (22%) or 11q (26%) occurred only in metastatic melanomas. A "background" rate (0-17%) of allele loss was seen on chromosomes 7, 17, and 21. These data strongly support the previous model based on karyotypic findings in melanocytic lesions. However, we have been able to further, augment that model by delimiting the regions of loss on 10q, to that distal to D10S254, and on 1p, to between D1S243 and D1S160.