Next generation sequencing and bioinformatics analysis of family genetic inheritance

AM Kanzi, JE San, B Chimukangara, E Wilkinson… - Frontiers in …, 2020 - frontiersin.org
Mendelian and complex genetic trait diseases continue to burden and affect society both
socially and economically. The lack of effective tests has hampered diagnosis thus, the …

Identification of de novo germline mutations and causal genes for sporadic diseases using trio‐based whole‐exome/genome sequencing

ZB **, Z Li, Z Liu, Y Jiang, XB Cai, J Wu - Biological Reviews, 2018 - Wiley Online Library
Whole‐genome or whole‐exome sequencing (WGS/WES) of the affected proband together
with normal parents (trio) is commonly adopted to identify de novo germline mutations …

Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks

J Su, Z Zheng, SS Ahmed, TW Lam… - Briefings in …, 2022 - academic.oup.com
Accurate identification of genetic variants from family child–mother–father trio sequencing
data is important in genomics. However, state-of-the-art approaches treat variant calling from …

Identification of novel genetic variants predisposing to familial oral squamous cell carcinomas

Y Huang, J Zhao, G Mao, GS Lee, J Zhang, L Bi, L Gu… - Cell Discovery, 2019 - nature.com
Oral squamous cell carcinoma (OSCC) is a common subtype of head and neck squamous
cell carcinoma (HNSCC), but the pathogenesis underlying familial OSCCs is unknown …

DeepTrio: variant calling in families using deep learning

A Kolesnikov, S Goel, M Nattestad, T Yun, G Baid… - bioRxiv, 2021 - biorxiv.org
Every human inherits one copy of the genome from their mother and another from their
father. Parental inheritance helps us understand the transmission of traits and genetic …

Dissecting the multifaceted contribution of the mitochondrial genome to autism spectrum disorder

L Caporali, C Fiorini, F Palombo, M Romagnoli… - Frontiers in …, 2022 - frontiersin.org
Autism spectrum disorder (ASD) is a clinically heterogeneous class of neurodevelopmental
conditions with a strong, albeit complex, genetic basis. The genetic architecture of ASD …

Parallel computing for genome sequence processing

Y Zou, Y Zhu, Y Li, FX Wu, J Wang - Briefings in Bioinformatics, 2021 - academic.oup.com
The rapid increase of genome data brought by gene sequencing technologies poses a
massive challenge to data processing. To solve the problems caused by enormous data and …

Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo

D Lähnemann, J Köster, U Fischer, A Borkhardt… - Nature …, 2021 - nature.com
Accurate single cell mutational profiles can reveal genomic cell-to-cell heterogeneity.
However, sequencing libraries suitable for genoty** require whole genome amplification …

dv-trio: a family-based variant calling pipeline using DeepVariant

EKK Ip, C Hadinata, JWK Ho, E Giannoulatou - Bioinformatics, 2020 - academic.oup.com
Abstract Motivation In 2018, Google published an innovative variant caller, DeepVariant,
which converts pileups of sequence reads into images and uses a deep neural network to …

[CARTE][B] Computational immunology: applications

S Ghosh - 2020 - taylorfrancis.com
Computational Immunology: Applications focuses on different mathematical models,
statistical tools, techniques, and computational modelling that helps in understanding …