Haplotype Counting by Next-Generation Sequencing for Ultrasensitive Human DNA Detection

Debeljak, Marija; Freed, Donald; Welch, Jane A.; Haley, Lisa; Beierl, Katie; Iglehart, Brian; Pallavajjala, Aparna; Gocke, Christopher D.; Leffell, Mary S.; Lin, Ming Tseh; Pevsner, Jonathan; Wheelan, Sarah J.; Eshleman, James R.

doi:10.1016/j.jmoldx.2014.04.003

Cited by 18 publications

(17 citation statements)

References 42 publications

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“…Biopsied tumors may be screened rapidly for putative driver mutations based on cancer type, informing treatment. Furthermore, once a cancer is in remission, tumor-specific DNA may be assayed at low cost with ultra-sensitive second-generation sequencing-based techniques [ 159 ]. These advances will likely improve prognosis for millions of cancer patients within the next decade.…”

Section: Somatic Mosaicism In Diseasementioning

confidence: 99%

Somatic Mosaicism in the Human Genome

Freed

Stevens

Pevsner

2014

Genes

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125

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Somatic mosaicism refers to the occurrence of two genetically distinct populations of cells within an individual, derived from a postzygotic mutation. In contrast to inherited mutations, somatic mosaic mutations may affect only a portion of the body and are not transmitted to progeny. These mutations affect varying genomic sizes ranging from single nucleotides to entire chromosomes and have been implicated in disease, most prominently cancer. The phenotypic consequences of somatic mosaicism are dependent upon many factors including the developmental time at which the mutation occurs, the areas of the body that are affected, and the pathophysiological effect(s) of the mutation. The advent of second-generation sequencing technologies has augmented existing array-based and cytogenetic approaches for the identification of somatic mutations. We outline the strengths and weaknesses of these techniques and highlight recent insights into the role of somatic mosaicism in causing cancer, neurodegenerative, monogenic, and complex disease.

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Section: Somatic Mosaicism In Diseasementioning

confidence: 99%

Somatic Mosaicism in the Human Genome

Freed

Stevens

Pevsner

2014

Genes

Self Cite

125

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“…15 These studies used digital melt-curve analysis and pyrosequencing to detect mutations but next-generation sequencing (NGS) is being widely used in clinical laboratories to detect somatic mutations in cancer tissues. 1617 …”

Section: Introductionmentioning

confidence: 99%

Digital next-generation sequencing identifies low-abundance mutations in pancreatic juice samples collected from the duodenum of patients with pancreatic cancer and intraductal papillary mucinous neoplasms

Sadakari

Shindo

et al. 2016

Gut

134

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Objective Secretin-stimulated pancreatic juice contains DNA shed from cells lining the pancreatic ducts. Genetic analysis of this fluid may form a test to detect pancreatic ductal neoplasia. Design We employed digital next-generation sequencing (‘digital NGS’) to detect low-abundance mutations in secretin-stimulated juice samples collected from the duodenum of subjects enrolled in Cancer of the Pancreas Screening studies at Johns Hopkins Hospital. For each juice sample, digital NGS necessitated 96 NGS reactions sequencing nine genes. The study population included 115 subjects (53 discovery, 62 validation) (1) with pancreatic ductal adenocarcinoma (PDAC), (2) intraductal papillary mucinous neoplasm (IPMN), (3) controls with non-suspicious pancreata. Results Cases with PDAC and IPMN were more likely to have mutant DNA detected in pancreatic juice than controls (both p<0.0001); mutant DNA concentrations were higher in patients with PDAC than IPMN (p=0.003) or controls (p<0.001). TP53 and/or SMAD4 mutations were commonly detected in juice samples from patients with PDAC and were not detected in controls (p<0.0001); mutant TP53/SMAD4 concentrations could distinguish PDAC from IPMN cases with 32.4% sensitivity, 100% specificity (area under the curve, AUC 0.73, p=0.0002) and controls (AUC 0.82, p<0.0001). Two of four patients who developed pancreatic cancer despite close surveillance had SMAD4/TP53 mutations from their cancer detected in juice samples collected over 1 year prior to their pancreatic cancer diagnosis when no suspicious pancreatic lesions were detected by imaging. Conclusions The detection in pancreatic juice of mutations important for the progression of low-grade dysplasia to high-grade dysplasia and invasive pancreatic cancer may improve the management of patients undergoing pancreatic screening and surveillance.

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“…Routine methods which are currently used for a-STR profiling based on standard PCR and capillary electrophoresis analysis have reached their sensitivity levels, while low levels mixtures remain problematic for comprehensive forensic analysis. But new methods of forensic analysis of mixed samples based on next generation sequencing, which are currently in phase of testing and implementation, will significantly improve sensitivity without loss of specificity of analysis [19,20]. This could lead to redefining of many analytical criteria for the successful identification of the perpetrator's DNA profile, not strictly based only on STR profiling as SNP or DIP analysis could be also applied.…”

Section: Discussionmentioning

confidence: 99%