ABSTRACT
The incidence of oesophagogastric junctional (OGJ) adenocarcinoma is rising rapidly in western countries, in contrast to the declining frequency of distal gastric carcinoma. Treatment options for adenocarcinomas involving the oesophagogastric junction are limited and the overall prognosis is extremely poor. To determine the genomic landscape of OGJ adenocarcinoma, exomes of eight tumours and matched germline DNA were subjected to massively parallel DNA sequencing. Microsatellite instability was observed in three tumours which coincided with an elevated number of somatic mutations. In total, 117 genes were identified that had predicted coding alterations in more than one tumour. Potentially actionable coding mutations were identified in 67 of these genes, including those in CR2, HGF , FGFR4, and ESRRB. Twenty-nine genes harbouring somatic coding mutations and copy number changes in the MSS OGJ dataset are also known to be altered with similar predicted functional consequence in other tumour types. Compared with the published mutational profile of gastric cancers, 49% (57/117) of recurrently mutated genes were unique to OGJ tumours. TP53, SYNE1, and ARID1A were amongst the most frequently mutated genes in a larger OGJ cohort. Our study provides an insight into the mutational landscape of OGJ adenocarcinomas and confirms that this is a highly mutated and heterogeneous disease. Furthermore, we have uncovered somatic mutations in therapeutically relevant genes which may represent candidate drug targets.
Subject(s)
Adenocarcinoma/genetics , DNA, Neoplasm/genetics , Esophageal Neoplasms/genetics , Esophagogastric Junction , Mutation , Stomach Neoplasms/genetics , Adaptor Proteins, Signal Transducing/analysis , Adaptor Proteins, Signal Transducing/genetics , Adenocarcinoma/chemistry , Adenocarcinoma/pathology , Adenosine Triphosphatases/analysis , Adenosine Triphosphatases/genetics , Adult , Aged , DNA Copy Number Variations/genetics , DNA Mutational Analysis , DNA Repair Enzymes/analysis , DNA Repair Enzymes/genetics , DNA-Binding Proteins/analysis , DNA-Binding Proteins/genetics , Esophageal Neoplasms/chemistry , Esophageal Neoplasms/pathology , Esophagogastric Junction/pathology , Exome/genetics , Female , Genome, Human/genetics , Humans , Immunohistochemistry , Loss of Heterozygosity/genetics , Male , Microsatellite Instability , Middle Aged , Mismatch Repair Endonuclease PMS2 , MutL Protein Homolog 1 , MutL Proteins , Mutation/genetics , Neoplasm Proteins/analysis , Neoplasm Proteins/genetics , Neoplasm Staging , Nuclear Proteins/analysis , Nuclear Proteins/genetics , Polymerase Chain Reaction/methods , Prospective Studies , Stomach Neoplasms/chemistry , Stomach Neoplasms/pathologyABSTRACT
BACKGROUND: A serious constraint in the investigation of the human platelet antigen (HPA) status of potential neonatal alloimmune thrombocytopenia (NAIT) cases is the limited amount of DNA available from the neonates. Whole genome amplification (WGA) of these DNA samples could overcome this problem, but requires validation to ensure that it is sufficiently sensitive and accurate before its application in a clinical diagnostic setting. STUDY DESIGN AND METHODS: This study has validated the use of WGA DNA for HPA-1, -2, -3, -4, -5, and -15 genotyping with a panel of six controls and 13 previously HPA-typed samples from neonates together with parental DNA, using a 5'-nuclease (TaqMan) assay. WGA was performed using titrated amounts of genomic and WGA DNA template. HPA typing was performed on genomic and amplified DNA using a 5'-nuclease assay or polymerase chain reaction with sequence-specific primers (PCR-SSP). RESULTS: WGA DNA yields were in the suggested range of 400x to 800x, as assessed by spectrophotometry and gel analysis, and did not require further purification. HPA genotyping showed 100 percent concordance when using down to 5 ng of genomic or WGA template. CONCLUSION: This study demonstrates that WGA can be used for HPA typing using PCR-SSP or plate-based 5'-nuclease assays. The use of WGA for HPA typing in clinical samples from NAIT patients was validated with 100 percent concordance, and it is suggested that this technology can be used for other analyses where DNA amounts are limited.
Subject(s)
Antigens, Human Platelet/genetics , Nucleic Acid Amplification Techniques/standards , Thrombocytopenia, Neonatal Alloimmune/diagnosis , DNA Primers , Genome, Human , Genotype , Humans , Infant, Newborn , Nucleic Acid Amplification Techniques/methods , Reagent Kits, DiagnosticABSTRACT
Increased mitochondrial DNA (mtDNA) copy number in peripheral blood cells (PBC) has been associated with the risk of developing several tumor types. Here we evaluate sources of variation of this biomarker and its association with breast cancer risk in a prospective cohort study. mtDNA copy number was measured using quantitative real-time PCR on PBC DNA samples from participants in the UK-based Breakthrough Generations Study. Temporal and assay variation was evaluated in a serial study of 91 women, with two blood samples collected approximately 6-years apart. Then, associations with breast cancer risk factors and risk were evaluated in 1,108 cases and 1,099 controls using a nested case-control design. In the serial study, mtDNA copy number showed low assay variation but large temporal variation [assay intraclass correlation coefficient (ICC), 79.3%-87.9%; temporal ICC, 38.3%). Higher mtDNA copy number was significantly associated with younger age at blood collection, being premenopausal, having an older age at menopause, and never taking HRT, both in cases and controls. Based on measurements in a single blood sample taken on average 6 years before diagnosis, higher mtDNA copy number was associated with increased breast cancer risk [OR (95% CI) for highest versus lowest quartile, 1.37 (1.02-1.83); P trend = 0.007]. In conclusion, mtDNA copy number is associated with breast cancer risk and represents a promising biomarker for risk assessment. The relatively large temporal variation should be taken into account in future analyses.
Subject(s)
Blood Cells/metabolism , Breast Neoplasms/genetics , DNA Copy Number Variations , DNA, Mitochondrial/genetics , Precancerous Conditions/genetics , Breast Neoplasms/blood , Case-Control Studies , Female , Follow-Up Studies , Genetic Predisposition to Disease , Humans , Middle Aged , Precancerous Conditions/blood , Risk FactorsABSTRACT
We conducted a genome-wide association study of male breast cancer comprising 823 cases and 2,795 controls of European ancestry, with validation in independent sample sets totaling 438 cases and 474 controls. A SNP in RAD51B at 14q24.1 was significantly associated with male breast cancer risk (P = 3.02 × 10(-13); odds ratio (OR) = 1.57). We also refine association at 16q12.1 to a SNP within TOX3 (P = 3.87 × 10(-15); OR = 1.50).