AIMC Topic: Exome Sequencing

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A machine-learning approach for accurate detection of copy number variants from exome sequencing.

Genome research
Copy number variants (CNVs) are a major cause of several genetic disorders, making their detection an essential component of genetic analysis pipelines. Current methods for detecting CNVs from exome-sequencing data are limited by high false-positive ...

Application of a Neural Network Whole Transcriptome-Based Pan-Cancer Method for Diagnosis of Primary and Metastatic Cancers.

JAMA network open
IMPORTANCE: A molecular diagnostic method that incorporates information about the transcriptional status of all genes across multiple tissue types can strengthen confidence in cancer diagnosis.

DeepPVP: phenotype-based prioritization of causative variants using deep learning.

BMC bioinformatics
BACKGROUND: Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In these methods, pathogenicity ...

MSIpred: a python package for tumor microsatellite instability classification from tumor mutation annotation data using a support vector machine.

Scientific reports
Microsatellite instability (MSI) is characterized by high degree of polymorphism in microsatellite lengths due to deficiency in mismatch repair (MMR) system. MSI is associated with several tumor types and its status can be considered as an important ...

A case of apolipoprotein A-I deficiency due to carboxyl-terminal truncation.

Journal of clinical lipidology
Apolipoprotein A-I deficiency is a rare metabolic disease characterized by an impaired reverse cholesterol transport system resulting in excessive cholesterol accumulation. Here, we discuss a case of apolipoprotein A-I deficiency caused by a carboxyl...

Divergent Clonal Evolution and Early Dissemination Promote Genetic Heterogeneity of Metastases in Castration-Resistant Prostate Cancer.

Cancer research
UNLABELLED: Lethal prostate cancer has passed through at least two evolutionary bottlenecks: acquisition of metastatic potential and development of castration resistance. A better understanding of how this affects genetic heterogeneity across metasta...

Whole Exome Sequencing on FHIR: Towards Adoption in Clinical Practice for Precision Oncology Pipelines.

Studies in health technology and informatics
INTRODUCTION: Whole Exome Sequencing (WES) promises to open a new range of personalized treatments due to breaking the limits of former panel-based methods of molecular analysis. While the methodology is well established and already included in clini...

Integrative exome sequencing and machine learning identify MICB and interferon pathway genes as contributors to SSc risk.

Annals of the rheumatic diseases
OBJECTIVES: Systemic sclerosis (SSc) is a complex autoimmune disease with both known and unidentified genetic contributors. While genome-wide association studies (GWAS) have implicated multiple loci, many reside in noncoding regions. We aimed to iden...

Leveraging Whole-Exome Sequencing and Mutational Signatures to Detect Homologous Recombination Deficiency in Cancer.

Cancer research
Homologous recombination is a high-fidelity DNA repair mechanism essential for maintaining genome stability. Impairment of this pathway, often due to BRCA1 or BRCA2 inactivation, leads to homologous recombination deficiency (HRD), forcing cells to re...

HRProfiler Detects Homologous Recombination Deficiency in Breast and Ovarian Cancers Using Whole-Genome and Whole-Exome Sequencing Data.

Cancer research
UNLABELLED: Breast and ovarian cancers harboring homologous recombination deficiency (HRD) are sensitive to PARP inhibitors and platinum chemotherapy. Conventionally, detecting HRD involves screening for defects in BRCA1, BRCA2, and other relevant ge...