Methods for copy number aberration detection from single-cell DNA-sequencing data
Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs),
play an important role in the initiation and progression of cancer. Single-cell DNA …
play an important role in the initiation and progression of cancer. Single-cell DNA …
Whole-genome CNV analysis: advances in computational approaches
M Pirooznia, FS Goes, PP Zandi - Frontiers in genetics, 2015 - frontiersin.org
Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a
significant contribution to human diversity and also play an important role in disease …
significant contribution to human diversity and also play an important role in disease …
CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are
of significant importance in syndromic conditions and cancer. Massively parallel sequencing …
of significant importance in syndromic conditions and cancer. Massively parallel sequencing …
Clonal expansion and diversification of cancer-associated mutations in endometriosis and normal endometrium
K Suda, H Nakaoka, K Yoshihara, T Ishiguro, R Tamura… - Cell reports, 2018 - cell.com
Endometriosis is characterized by ectopic endometrial-like epithelium and stroma, of which
molecular characteristics remain to be fully elucidated. We sequenced 107 ovarian …
molecular characteristics remain to be fully elucidated. We sequenced 107 ovarian …
Whole-organism clone tracing using single-cell sequencing
Embryonic development is a crucial period in the life of a multicellular organism, during
which limited sets of embryonic progenitors produce all cells in the adult body. Determining …
which limited sets of embryonic progenitors produce all cells in the adult body. Determining …
Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries
Neuroblastoma is a tumor of the peripheral sympathetic nervous system, derived from
multipotent neural crest cells (NCCs). To define core regulatory circuitries (CRCs) controlling …
multipotent neural crest cells (NCCs). To define core regulatory circuitries (CRCs) controlling …
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
M Cretu Stancu, MJ Van Roosmalen, I Renkens… - Nature …, 2017 - nature.com
Despite improvements in genomics technology, the detection of structural variants (SVs)
from short-read sequencing still poses challenges, particularly for complex variation. Here …
from short-read sequencing still poses challenges, particularly for complex variation. Here …
Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)
Single-cell genomics is important for biology and medicine. However, current whole-
genome amplification (WGA) methods are limited by low accuracy of copy-number variation …
genome amplification (WGA) methods are limited by low accuracy of copy-number variation …
Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer
CL Hodgkinson, CJ Morrow, Y Li, RL Metcalf… - Nature medicine, 2014 - nature.com
Small-cell lung cancer (SCLC), an aggressive neuroendocrine tumor with early
dissemination and dismal prognosis, accounts for 15–20% of lung cancer cases and∼ …
dissemination and dismal prognosis, accounts for 15–20% of lung cancer cases and∼ …
DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning
Microscopy image analysis is a major bottleneck in quantification of single-cell microscopy
data, typically requiring human oversight and curation, which limit both accuracy and …
data, typically requiring human oversight and curation, which limit both accuracy and …