David Haan
A5002402867- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Pancreatic and Hepatic Oncology Research
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- Genetic factors in colorectal cancer
- Lung Cancer Treatments and Mutations
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Cancer, Hypoxia, and Metabolism
- Molecular Biology Techniques and Applications
- Genomics and Rare Diseases
- Evolution and Genetic Dynamics
- Cancer Immunotherapy and Biomarkers
- Nutrition, Genetics, and Disease
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Mitochondrial Function and Pathology
- Cancer-related gene regulation
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Chromosomal and Genetic Variations
- Adrenal and Paraganglionic Tumors
- Cholangiocarcinoma and Gallbladder Cancer Studies
- RNA Research and Splicing
University of California, Santa Cruz
2016-2023
ID Genomics (United States)
2020-2023
Abstract A key mutational process in cancer is structural variation, which rearrangements delete, amplify or reorder genomic segments that range size from kilobases to whole chromosomes 1–7 . Here we develop methods group, classify and describe somatic variants, using data the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium International Cancer Genome (ICGC) The Atlas (TCGA), aggregated whole-genome sequencing 2,658 cancers across 38 tumour types 8 Sixteen signatures variation...
Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies selected types have suggested chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium International Cancer Genome (ICGC) The Atlas (TCGA), we analyze patterns across 2,658 tumors 38 using whole-genome sequencing We find...
Multi-omics datasets represent distinct aspects of the central dogma molecular biology. Such high-dimensional profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple using statistical fusion, rationalizes contributing evidence highlights associated genes. As part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing from...
Abstract Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative lengthening associated with ATRX DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium , we dissect whole-genome sequencing data over 2500 matched tumor-control samples from 36 different tumor types aggregated within to characterize genomic footprints these mechanisms. While content tumors mutations...
Abstract The catalog of cancer driver mutations in protein-coding genes has greatly expanded the past decade. However, non-coding are less well-characterized and only a handful recurrent mutations, most notably TERT promoter have been reported. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 across 38 tumor types, we perform multi-faceted pathway network analyses 2583 genomes 27 types compiled by PCAWG...
Abstract The discovery of driver mutations is one the key motivations for cancer genome sequencing. Here , as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium which aggregated whole sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify in coding non-coding sites within genomes. Using total 1373 genomic features derived public sources, DriverPower’s...
The American alligator, Alligator mississippiensis, like all crocodilians, has temperature-dependent sex determination, in which the of an embryo is determined by incubation temperature egg during a critical period development. lack genetic differences between male and female alligators leaves open question how genes responsible for determination differentiation are regulated. Insight into this comes from fact that exposing incubated at male-producing to estrogen causes it develop ovaries....
The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from inference impacts somatic variants to pathway analysis biomarker development subtype discovery. ICGC-TCGA DREAM Somatic Mutation Calling (SMC-RNA) challenge was a crowd-sourced effort benchmark methods isoform quantification fusion detection bulk sequencing (RNA-seq) data. It concluded 2018 with comparison 77 entries 65 on 51 synthetic tumors 32 cell lines...
RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) characterize the minority LUADs lacking apparent in pathway. We show that WGS analysis uncovers RPA(+) 28 (33%) samples. Among remaining 57 cases, observe focal deletions targeting promoter or transcription start site STK11 (n = 7) KEAP1 3), and mutations associated with...
Early detection of pancreatic cancer has been shown to improve patient survival rates. However, effective early tools detect do not currently exist. The Avantect Pancreatic Cancer Test, leveraging the 5-hydroxymethylation [5-hydroxymethylcytosine (5hmC)] signatures in cell-free DNA, was developed and analytically validated address this unmet need. We report a comprehensive analytical validation study encompassing precision, sample stability, limit detection, interfering substance studies,...
While advancements in genome sequencing have identified millions of somatic mutations cancer, their functional impact is poorly understood. We previously developed the expression-based variant phenotyping (eVIP) method to use gene expression data characterize function variants. The eVIP uses a decision tree-based algorithm predict variants by comparing signatures induced introduction wild-type (WT) versus mutant cDNAs cell lines. distinguishes between that are gain-of-function,...
Abstract The catalog of cancer driver mutations in protein-coding genes has greatly expanded the past decade. However, non-coding are less well-characterized and only a handful recurrent mutations, most notably TERT promoter have been reported. Motivated by success pathway network analyses prioritizing rare genes, we performed multi-faceted across 2,583 whole genomes from 27 tumor types compiled ICGC/TCGA PCAWG project. While few genomic elements were recurrently mutated this cohort,...
Abstract Background: Pancreatic cystic lesions are common incidental findings on imaging, but up to half may be precursors of pancreatic cancer. Current diagnostic methods cannot robustly identify cysts that have the highest probability progress cancer and require treatment. To address this gap, we evaluated performance a non-invasive epigenomic based test employing cell-free DNA, Avantect Cancer test, in cohort patients with those at higher risk malignancy. Methods: In study, investigated...
Abstract Background: Epigenomic changes via the measurement of 5-hydroxymethylation cytosine (5hmC) in DNA have been shown to enable detection a variety cancers including pancreatic and ovarian cancer plasma-derived cell-free (cfDNA). Here, we investigated whether blood-based 5hmC profiling genomic (gDNA) derived from cells buffy coat (BC) possess signals that breast, colorectal lung cancers. Method: Blood samples collected Streck tubes patients or non-cancer controls were processed obtain...
672 Background: Pancreatic cancer is one of the deadliest cancers, with approximately 15-20% patients who present at diagnosis a resectable disease. The major barrier to better outcomes lack early-detection molecular tools enable timely intervention. We have developed test that enables detection pancreatic from simple blood draw. incorporates novel, genome-wide sequencing-based epigenomics method enriches for DNA loci undergo active de-methylation. measurement 5-hydroxymethylcytosine (5hmC)...
Abstract The American alligator, Alligator mississippiensis , like all crocodilians, has temperature-dependent sex determination, in which the of an embryo is determined by incubation temperature egg during a critical period development. lack genetic differences between male and female alligators leaves open question how genes responsible for determination differentiation are regulated. One insight into this comes from fact that exposing incubated at male-producing to estrogen causes it...