Transflip mutations produce deletions in pancreatic cancer

Norris, Alexis L.; Kamiyama, Hirohiko; Makohon-Moore, Alvin; Pallavajjala, Aparna; Morsberger, Laura; Lee, Kurt; Batista, Denise; Iacobuzio‐Donahue, Christine A.; Lin, Ming Tseh; Klein, Alison P.; Hruban, Ralph H.; Wheelan, Sarah J.; Eshleman, James R.

doi:10.1002/gcc.22258

Cited by 11 publications

(14 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Translocations most frequently affected chromosomes harbouring key pancreatic tumour suppressors, such as CDKN2A (Chr9) or P53 (Chr17). In accordance, recent evidence suggests that structural variations in PDAC are non-random: inter-chromosomal translocations, for example, are predominantly unbalanced and typically affect (disrupt) key tumour suppressor genes, including CKDN2A , SMAD4 or P53 (refs 37 , 38 , 39 ).…”

Section: Resultsmentioning

confidence: 55%

Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice

et al. 2016

View full text Add to dashboard Cite

Mouse transgenesis has provided fundamental insights into pancreatic cancer, but is limited by the long duration of allele/model generation. Here we show transfection-based multiplexed delivery of CRISPR/Cas9 to the pancreas of adult mice, allowing simultaneous editing of multiple gene sets in individual cells. We use the method to induce pancreatic cancer and exploit CRISPR/Cas9 mutational signatures for phylogenetic tracking of metastatic disease. Our results demonstrate that CRISPR/Cas9-multiplexing enables key applications, such as combinatorial gene-network analysis, in vivo synthetic lethality screening and chromosome engineering. Negative-selection screening in the pancreas using multiplexed-CRISPR/Cas9 confirms the vulnerability of pancreatic cells to Brca2-inactivation in a Kras-mutant context. We also demonstrate modelling of chromosomal deletions and targeted somatic engineering of inter-chromosomal translocations, offering multifaceted opportunities to study complex structural variation, a hallmark of pancreatic cancer. The low-frequency mosaic pattern of transfection-based CRISPR/Cas9 delivery faithfully recapitulates the stochastic nature of human tumorigenesis, supporting wide applicability for biological/preclinical research.

show abstract

Section: Resultsmentioning

confidence: 55%

Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice

et al. 2016

View full text Add to dashboard Cite

show abstract

“…33,[41][42][43] Complex SVs have been found to cause approximately half of nucleotide deletions in pancreatic ductal adenocarcinoma (PDAC). [44][45][46] Furthermore, CDKN2A/p16 and SMAD4/DPaazC4 have been identied as two of the most common deleted tumor suppressor genes. The ability to detect these mutations is critically important to the healthcare industry, allowing the monitoring of cancer patients for early detection of possible relapse.…”

Section: Structural Variantsmentioning

confidence: 99%

“…The ability to detect these mutations is critically important to the healthcare industry, allowing the monitoring of cancer patients for early detection of possible relapse. 33,[44][45][46][47] In mammalian cells with highly repetitive genomes, studies of SVs frequently use a resequencing approach, in which the read from the target genome is independently aligned from the reference genome to search for SVs. 48 In general, besides specicity and sensitivity, when detecting SVs, a method's quality is further judged by its ability to accurately predict breakpoint locations, the size of variants, and changes in copy count.…”

Section: Structural Variantsmentioning

confidence: 99%

Piecing together the puzzle: nanopore technology in detection and quantification of cancer biomarkers

Davidson

Borgesi

et al. 2017

RSC Adv.

View full text Add to dashboard Cite

Cancer is the result of a multistep process, including various genetic and epigenetic alterations, such as structural variants, transcriptional factors, telomere length, DNA methylation, histone-DNA modification, and aberrant expression of miRNAs. These changes cause gene defects in one of two ways: (1) gain in function which shows enhanced expression or activation of oncogenes, or (2) loss of function which shows repression or inactivation of tumor-suppressor genes. However, most conventional methods for screening and diagnosing cancers require highly trained experts, intensive labor, large counter space (footprint) and extensive capital costs. Consequently, current approaches for cancer detection are still considered highly novel and are not yet practically applicable for clinical usage. Nanopore-based technology has grown rapidly in recent years, which have seen the wide application of biosensing research to a number of life sciences. In this review paper, we present a comprehensive outline of various genetic and epigenetic causal factors of cancer at the molecular level, as well as the use of nanopore technology in the detection and study of those specific factors. With the ability to detect both genetic and epigenetic alterations, nanopore technology would offer a cost-efficient, labor-free and highly practical approach to diagnosing pre-cancerous stages and early-staged tumors in both clinical and laboratory settings.

show abstract

“…6 These 10 SVs included 2 interstitial deletions, 4 translocations, 4 inversions, and 1 combination of an inversion and translocation ("TransFlip" mutations, Table 1). Wildtype (WT) sequence (intact genomic sequence; no SV) served as a control and one SV (SV01) had a technical replicate (SV07).…”

Section: Ability To Detect Simple and Complex Svsmentioning

confidence: 99%

“…CDKN2A/p16 and SMAD4/DPC4 are 2 of the most commonly deleted TSGs in human cancer, and complex SVs have been found to underlie approximately half of these deletions in pancreatic ductal adenocarcinoma (PDAC). [4][5][6] The sensitive detection of tumor-specific mutations, including both small alterations such as single base substitutions and large alterations such as SVs, of circulating tumor DNA is critical for applications such as molecular relapse, 7 early detection, 8 and possibly therapeutic monitoring of cancer patients. 9 The arrival of 2nd generation sequencing has provided ample opportunity to investigate small alterations, but the large SV alterations remain under-studied because of the difficulty detecting them with the short reads (<300 bp) of 2nd generation sequencing.…”

Section: Introductionmentioning

confidence: 99%

Nanopore sequencing detects structural variants in cancer

Norris

Workman

Fan

et al. 2015

Preprint

Self Cite

View full text Add to dashboard Cite

Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300 bp) of 2nd generation sequencing. Not only do the reads (or paired-end reads) need to straddle a breakpoint, but repetitive elements often lead to ambiguities in the alignment of short reads. We propose to use the long-reads (up to 20 kb) possible with 3rd generation sequencing, specifically nanopore sequencing on the MinION. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Though nanopore sequencing currently has a relatively high mismatch rate that precludes base substitution and small frameshift mutation detection, its accuracy is sufficient for SV detection because of its long reads. In fact, long reads in some cases may improve SV detection efficiency.We have tested nanopore sequencing to detect a series of well-characterized SVs, including large deletions, inversions, and translocations that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we have demonstrated that nanopore sequencing can detect large deletions, translocations and inversions at dilutions as low as 1:100, with as few as 500 reads per sample. Given the speed, small footprint, and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of cancer-associated SVs needed for molecular relapse, early detection, or therapeutic monitoring.

show abstract

Transflip mutations produce deletions in pancreatic cancer

Cited by 11 publications

References 28 publications

Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice

Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice

Piecing together the puzzle: nanopore technology in detection and quantification of cancer biomarkers

Nanopore sequencing detects structural variants in cancer

Contact Info

Product

Resources

About