Journal:

Article Title: The impact of next-generation sequencing on genomics

doi: 10.1016/j.jgg.2011.02.003

Figure Lengend Snippet: The end-user software packages and cloud computing software for NGS data analysis.

Article Snippet: GenomeQuest, Complete Genomics and Geospiza/GeneSifter provide online customer oriented NGS data analysis services, which is a little different from cloud computing by definition.

Techniques: Software, Modification

Journal: Journal of Medical Genetics

Article Title: Hiding in plain sight: a partial deletion of BRCA1 exon 7 undetectable by MLPA is a Nepali founder variant

doi: 10.1136/jmg-2024-110422

Figure Lengend Snippet: Founder deletion in BRCA1 with 3 different annotations in ClinVar ( www.ncbi.nlm.nih.gov/clinvar ; data accessed 31 Jul 2024)

Article Snippet: Ethnicity of families and other information provided by submitter , Tested individuals were of Nepalese descent. Variant detected in NGS data using split-reads. No confirmation method as MLPA probes do not overlap the deletion. However, NGS reads are of good enough quality to be confident that it is a true positive call (Labcorp Genetics, formerly Invitae, personal communication, 2023). , First submission relates to two clients, but neither provided ancestry information. Deletion identified with both Scalpel and an in-house developed split-read algorithm (Color Health, personal communication, 2023).For second submission, tested individuals were of Nepalese descent. Variant detected in NGS data using split-reads and validated using PacBio (Labcorp Genetics, formerly Invitae, personal communication, 2023). , The proband in this family was diagnosed with ovarian cancer in her early 50s and does appear to have Nepalese ancestry. Three additional family members were found to be carriers but have no personal history of cancer at the time of testing in their 30s to 40s. Picked up by NGS pipeline and then Sanger validated (Ambry Genetics, personal communication, 2024).Variant.

Techniques: Variant Assay

Journal: bioRxiv

Article Title: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

doi: 10.1101/2020.01.31.928796

Figure Lengend Snippet: Genome Detective Coronavirus Typing Tool assembles genomes from next generation sequencing (NGS) in FASTAQ format or assembled genomes in FASTA format. A user can submit up to 1Gb of NGS data or 2,000 assembled genomic sequences. For each assembled genomic sequence, the tool identifies the virus species, constructs a phylogenetic tree and identifies phylogenetic clusters, which includes the novel coronavirus identified in Wuhan China in 2019 (2019-nCoV). The tool identifies changes at nucleotides, coding regions and proteins using a novel dynamic aligner and display all of the mutations in detailed tables and reports.

Article Snippet: It accepts assembled genomes in FASTA format or raw NGS data in FASTQ format from Illumina, Ion Torrent, PACBIO or Oxford Nanopore Technologies (ONT) can be submitted to the Genome Detective Virus Tool ( ) to automatically assemble the consensus genome prior to executing the Coronavirus Typing Tool.

Techniques: Next-Generation Sequencing, Genomic Sequencing, Sequencing, Virus, Construct

Journal: BioMed Research International

Article Title: Potential of Using Cell-Free DNA and miRNA in Breast Milk to Screen Early Breast Cancer

doi: 10.1155/2020/8126176

Figure Lengend Snippet: Identification of BM cfRNA deriving mainly from breast-derived cells. RNAs of BM cfRNAs and BM cellular RNA from three different donors (donors 7, 8, and 9) were subjected to RT-PCR to detect mRNA levels of (a) highly expressed genes in breast-related and (b) highly expressed genes in blood-related cells. The graphs show normalized −ΔCt values for the indicated genes (described in detail in Supplemental Text). All error bars denote SEM, n = 3. (c) The heat map of methylation levels in every identical reliable slide window of different samples. WGBS data was analyzed with default parameters (1000 bp slide windows, 500 bp overlap). For accuracy, only slide windows with more than 3000 total C reads (methylated and unmethylated) were regarded as reliable for comparison between samples. The graph was drawn with Log2 methylated percentages after mean subtraction and standardization and arranged in descending order across all chromosomes of the gDNA6 sample. (d) The chromosome-separated heat map of methylation levels in identical reliable slide windows of different samples. The graph was drawn with Log2 methylated percentages after mean subtraction and standardization and arranged in descending order in each chromosome of the gDNA6 sample.

Article Snippet: miRNA sequencing and whole genome bisulfite sequencing (WGBS) were performed by LC Sciences (Houston, TX, USA).

Techniques: Derivative Assay, Reverse Transcription Polymerase Chain Reaction, Methylation, Comparison