Structural variant calling: the long and the short of it

M Mahmoud, N Gobet, DI Cruz-Dávalos, N Mounier… - Genome biology, 2019 - Springer
Recent research into structural variants (SVs) has established their importance to medicine
and molecular biology, elucidating their role in various diseases, regulation of gene …

Computational analysis of cancer genome sequencing data

I Cortés-Ciriano, DC Gulhan, JJK Lee… - Nature Reviews …, 2022 - nature.com
Distilling biologically meaningful information from cancer genome sequencing data requires
comprehensive identification of somatic alterations using rigorous computational methods …

The genomic landscape of pediatric acute lymphoblastic leukemia

SW Brady, KG Roberts, Z Gu, L Shi, S Pounds, D Pei… - Nature …, 2022 - nature.com
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Here, using
whole-genome, exome and transcriptome sequencing of 2,754 childhood patients with ALL …

Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution

M Chan-Seng-Yue, JC Kim, GW Wilson, K Ng… - Nature …, 2020 - nature.com
Pancreatic adenocarcinoma presents as a spectrum of a highly aggressive disease in
patients. The basis of this disease heterogeneity has proved difficult to resolve due to poor …

Organoid profiling identifies common responders to chemotherapy in pancreatic cancer

H Tiriac, P Belleau, DD Engle, D Plenker, A Deschênes… - Cancer discovery, 2018 - AACR
Pancreatic cancer is the most lethal common solid malignancy. Systemic therapies are often
ineffective, and predictive biomarkers to guide treatment are urgently needed. We generated …

Genomes for kids: the scope of pathogenic mutations in pediatric cancer revealed by comprehensive DNA and RNA sequencing

S Newman, J Nakitandwe, CA Kesserwan, EM Azzato… - Cancer discovery, 2021 - AACR
Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-
risk disease. Here, we used a three-platform sequencing approach, including whole …

Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma

A Jusakul, I Cutcutache, CH Yong, JQ Lim, MN Huang… - Cancer discovery, 2017 - AACR
Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in
countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries …

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing

S Kosugi, Y Momozawa, X Liu, C Terao, M Kubo… - Genome biology, 2019 - Springer
Abstract Background Structural variations (SVs) or copy number variations (CNVs) greatly
impact the functions of the genes encoded in the genome and are responsible for diverse …

A new genomic framework to categorize pediatric acute myeloid leukemia

M Umeda, J Ma, T Westover, Y Ni, G Song… - Nature Genetics, 2024 - nature.com
Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific
driver alterations, many of which are underrepresented in the current classification schemas …

Germline mutations in predisposition genes in pediatric cancer

J Zhang, MF Walsh, G Wu, MN Edmonson… - … England Journal of …, 2015 - Mass Medical Soc
Background The prevalence and spectrum of predisposing mutations among children and
adolescents with cancer are largely unknown. Knowledge of such mutations may improve …