Clarence Lee
A5008515166- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Digital Marketing and Social Media
- Gut microbiota and health
- RNA Research and Splicing
- Technology Adoption and User Behaviour
- Cystic Fibrosis Research Advances
- Cancer-related molecular mechanisms research
- Epigenetics and DNA Methylation
- Genomic variations and chromosomal abnormalities
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- Genetic factors in colorectal cancer
- Microbial Community Ecology and Physiology
- Consumer Market Behavior and Pricing
- Genomics and Chromatin Dynamics
- Parasites and Host Interactions
- Human Pose and Action Recognition
- Multimodal Machine Learning Applications
- Wildlife Ecology and Conservation
- Digital Media Forensic Detection
- Customer churn and segmentation
- Acute Myeloid Leukemia Research
- Genetic Associations and Epidemiology
Oregon Health & Science University
2022
Cornell University
2017-2022
University of the District of Columbia
2021
University Hospital Schleswig-Holstein
2019
University of Lübeck
2019
Kiel University
2019
Howard University
2009-2018
Morehouse School of Medicine
2017
SC Johnson (United States)
2017
Thermo Fisher Scientific (United States)
2014-2016
The development of noninvasive methods to detect and monitor tumors continues be a major challenge in oncology. We used digital polymerase chain reaction-based technologies evaluate the ability circulating tumor DNA (ctDNA) 640 patients with various cancer types. found that ctDNA was detectable >75% advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, head neck cancers, but less than 50% primary brain, renal, prostate, or thyroid cancers. In...
Cancer is driven by mutation. Worldwide, tobacco smoking the principal lifestyle exposure that causes cancer, exerting carcinogenicity through >60 chemicals bind and mutate DNA. Using massively parallel sequencing technology, we sequenced a small-cell lung cancer cell line, NCI-H209, to explore mutational burden associated with smoking. A total of 22,910 somatic substitutions were identified, including 134 in coding exons. Multiple mutation signatures testify cocktail carcinogens smoke their...
Spatial and temporal dissection of the genomic changes occurring during evolution human non-small cell lung cancer (NSCLC) may help elucidate basis for its dismal prognosis. We sequenced 25 spatially distinct regions from seven operable NSCLCs found evidence branched evolution, with driver mutations arising before after subclonal diversification. There was pronounced intratumor heterogeneity in copy number alterations, translocations, associated APOBEC cytidine deaminase activity. Despite...
High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental populations and present an approach for combining complementary aspects whole-genome, low-coverage data targeted high-coverage data. We apply this to generated by pilot phase Thousand Genomes Project, including whole-genome 2–4× coverage 179 samples from HapMap European, Asian, African panels as well target exons 800...
Carrier testing for 448 severe childhood recessive diseases by next-generation sequencing has good predictive value and suggests that every individual carries about three disease mutations.
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one each of the putative centers domestication, two basal lineages (Basenji Dingo) a golden jackal as an outgroup. Analysis these supports demographic model in which dogs wolves diverged through dynamic process involving population bottlenecks both post-divergence gene flow. In dogs, bottleneck involved at least 16-fold...
We describe the genome sequencing of an anonymous individual African origin using a novel ligation-based assay that enables unique form error correction improves raw accuracy aligned reads to >99.9%, allowing us accurately call SNPs with as few two per allele. collected several billion mate-paired yielding ∼18× haploid coverage sequence and close 300× clone coverage. Over 98% reference is covered at least one uniquely placed read, 99.65% spanned by clone. identify over 3.8 million SNPs,...
Rapid detection of specific aberrant rearrangements in tumors from individuals yields a well-poised technological advance toward personalized oncology.
The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass Italian part of Ötztal Alps. Here we report complete genome sequence Iceman and show 100% concordance between previously reported mitochondrial consensus generated from our genomic data. We present indications for recent common ancestry present-day inhabitants Tyrrhenian Sea, that probably had brown eyes, belonged to blood group O lactose intolerant. His genetic predisposition shows an...
Abstract Background Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance these variants remains controversial. Observational studies show that isomiR patterns non-random, hinting molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for molecules. Results To assess relevance we have performed ultra-deep miRNA-seq on ten adult human tissues, created...
Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the composition of directly patients, without need prior culture. have combined semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 2 (∼360 bp) with de-noising pipeline...
Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the process cannot be easily identified traditional tools. We show that high-throughput, massively parallel sequencing technologies can completely accurately characterize a mutant genome relative to previously sequenced parental (reference) strain. studied strain of Pichia stipitis, yeast capable...
Abnormalities of genomic methylation patterns are lethal or cause disease, but the cues that normally designate CpG dinucleotides for poorly understood. We have developed a new method profiling has single-CpG resolution and can address status repeated sequences. used this to determine >275 million sites in human mouse DNA from breast brain tissues. Methylation density at most sequences was found increase linearly with fall sharply very high densities, transposons remained densely methylated...
The somatic mutation burden in healthy white blood cells (WBCs) is not well known. Based on deep whole-genome sequencing, we estimate that approximately 450 mutations accumulated the nonrepetitive genome within compartment of a 115-yr-old woman. detected appear to have been harmless passenger mutations: They were enriched noncoding, AT-rich regions are evolutionarily conserved, and they depleted for genomic elements where might favorable or adverse effects cellular fitness, such as with...
Objective. Breath testing and duodenal culture studies suggest that a significant proportion of irritable bowel syndrome (IBS) patients have small intestinal bacterial overgrowth. In this study, we extended these data through 16S rDNA amplicon sequencing quantitative PCR (qPCR) analyses aspirates from large cohort IBS, non-IBS control subjects. Materials methods. Consecutive subjects presenting for esophagogastroduodenoscopy only healthy controls were recruited. Exclusion criteria included...
Controlling for background demographic effects is important accurately identifying loci that have recently undergone positive selection. To date, the of demography not yet been explicitly considered when under selection during dog domestication. investigate on lineage early in domestication, we examined patterns polymorphism six canid genomes were previously used to infer a model Using an inferred model, computed false discovery rates (FDR) and identified 349 outlier regions consistent with...
Noninvasive prenatal diagnosis of trisomy 21 (T21) has recently been shown to be achievable by massively parallel sequencing maternal plasma on a sequencing-by-synthesis platform. The quantification several other human chromosomes, including chromosomes 18 and 13, less precise, however, with quantitative biases related the chromosomal GC content.Maternal DNA from 10 euploid 5 T21 pregnancies was sequenced sequencing-by-ligation approach. We calculated genomic representations (GRs) reads each...
Intra-tumor heterogeneity is a hallmark of many cancers and may lead to therapy resistance or interfere with personalized treatment strategies. Here, we combined topographic mapping somatic breakpoints transcriptional profiling probe intra-tumor treatment-naïve stage IIIC/IV epithelial ovarian cancer. We observed that most substantial differences in genomic rearrangement landscapes occurred between metastases the omentum peritoneum versus tumor sites ovaries. Several cancer genes such as NF1...
Independent determination of both haplotype sequences an individual genome is essential to relate genetic variation function, phenotype, and disease. To address the importance phase, we have generated most complete haplotype-resolved date, “Max Planck One” (MP1), by fosmid pool-based next generation sequencing. Virtually all SNPs (>99%) 80,000 indels were phased into haploid up 6.3 Mb (N50 ∼1 Mb). The completeness phasing allowed concrete molecular pairs for vast majority genes (81%)...
The mangrove rivulus (Kryptolebias marmoratus) is one of two preferentially self-fertilizing hermaphroditic vertebrates.This mode reproduction makes an important model for evolutionary and biomedical studies because long periods selffertilization result in naturally homozygous genotypes that can produce isogenic lineages without significant limitations associated with inbreeding depression.Over 400 currently held laboratories across the globe show considerable amonglineage variation...
The authors propose a new Bayesian synthetic control framework to overcome limitations of extant methods (SCMs). proposed (BSCMs) do not impose any restrictive constraints on the parameter space priori. Moreover, they provide statistical inference in straightforward manner as well natural mechanism deal with “large p, small n” and sparsity problems through Markov chain Monte Carlo procedures. Using simulations, find that for variety data-generating processes, BSCMs almost always better...