lect 22 Overview of Sequencing and Next-Generation Sequencing (NGS)

Practice flashcards covering DNA sequencing technologies, applications of NGS, bioinformatic analysis, and clinical case studies including Fetal Akinesia and CMT.

Sanger Sequencing

A method of DNA sequencing used to determine the nucleotide sequence of DNA, characterized by its specific process, advantages, and limitations which are often compared to newer technologies like pyrosequencing.

Exome Sequencing

A single method used to sequence over $250\,000$ exons, involving solution-phase oligonucleotide hybridisation, typically sequencing $45.1\,Mb$ of DNA per individual.

Nimblegen capture array

A specific tool used to fragment and hybridize genomic DNA (gDNA) specifically for capturing exons during the process of exome sequencing.

GnomAD / ExAC

Population genetics databases used during data processing to filter variants by frequency for identifying potential disease-causing mutations.

Transcriptome sequencing

An application of next-generation sequencing used for the quantification of gene expression, alternative splicing, transcript annotation, and the discovery of transcribed SNPS or somatic mutations.

Metagenomic sequencing

The use of NGS for the discovery of infectious and commensal flora within a sample.

ChIP-Seq (Chromatin immunoprecipitation-sequencing)

A technique used for genome-wide mapping of protein-DNA interactions.

Glycogen-Branching Enzyme 1 ($GBE1$)

The gene where variants, including the missense mutation $His319Arg$, can lead to Glycogen Storage Disease type IV ($GSD\,IV$), also known as Andersen disease.

Fetal Akinesia

A rare group of genetically heterogeneous disorders characterized by decreased movement in utero, intrauterine growth restriction, craniofacial anomalies, and joint contractures.

Charcot-Marie-Tooth Disease ($CMT$)

A common inherited peripheral neuropathy involving mutations in $54$ known genes, clinically characterized by distal wasting of legs and hands, and skeletal deformations like pes cavus and hammer toes.

$AARS$ (alanyl-tRNA synthetase)

A gene located on chromosome $16$ identified via linkage analysis as a cause for autosomal dominant Charcot-Marie-Tooth disease when mutated (e.g., variant $p.R329H$).

$mTOR$ (mammalian target of rapamycin)

A gene where a $p.Glu1799Lys$ missense mutation in the kinase domain was identified in patients with developmental delay, dysmorphia, and macrocephaly.

Bisulfite-treated DNA sequencing

A specific NGS application used for determining patterns of cytosine methylation in genomic DNA.

Paired end sequencing

A sequencing approach used for the discovery of inherited and acquired structural variation.

Molecular barcoding

A technique that allows for multiplex sequencing of samples from multiple individuals simultaneously.