massive parallel amplicon sequencing  (Novogene)

Journal: eLife

Article Title: Unbiased mosaic variant assessment in sperm: a cohort study to test predictability of transmission

doi: 10.7554/eLife.78459

Figure Lengend Snippet: ( a ) Overview of the employed workflow from mutation detection to validation and prediction. A single massive parallel amplicon sequencing (MPAS) panel was used for both detections of mutations in parental tissues and in preimplantation blastocysts. WGS: whole-genome sequencing; 300× MSMF: variant calling pipeline on 300× WGS data using MuTect2, Strelka2, and MosaicForecast . ( b ) The number of MPAS-validated gonadal mosaic mutations for each sperm donor, distinguished by color into sperm-specific (‘ Sperm ’, green) and tissue-shared (‘ Shared ’, brown) mutations. ( c ) Ranked plot of all gonadal mosaic mutations across the three sperm donors. For each variant, both the allelic fraction (AF; normalized to chromosome count) of the mutation in sperm (green line) and in the soma (brown dot) are shown together with their 95% exact confidence interval. Shared mutations tend to be of higher AF compared to Sperm .

Article Snippet: All putative mosaic mutations (single-nucleotide variants and small insertion–deletion mutations only) as well as 120 common and rare single-nucleotide polymorphisms (SNPs), each detected as heterozygous in only one of the sperm donors, were then subjected to validation using massive parallel amplicon sequencing (MPAS, AmpliSeq Illumina Custom DNA Panel), to orthogonally assess each mutation in sperm donors, egg donors, and blastocysts.

Techniques: Mutagenesis, Biomarker Discovery, Amplification, Sequencing, Variant Assay

Journal: bioRxiv

Article Title: Sperm mosaicism predicts transmission of de novo mutations to human blastocysts

doi: 10.1101/2022.03.28.486034

Figure Lengend Snippet: Detection of gonadal mosaicism in three sperm donors. (a) Overview of the employed workflow from mutation detection to validation and prediction. A single massive parallel amplicon sequencing (MPAS) panel was used for both detections of mutations in parental tissues and in preimplantation blastocysts. WGS: whole genome sequencing; 300×MSMF: variant calling pipeline on 300× WGS data using MuTect2, Strelka2, and MosaicForecast . (b) Number of MPAS-validated gonadal mosaic mutations for each sperm donor, distinguished by color into sperm-specific (‘ Sperm’ , green) and tissue-shared (‘ Shared’ , brown) mutations. (c) Ranked plot of all gonadal mosaic mutations across the three sperm donors. For each variant, both the allelic fraction (AF; normalized to chromosome count) of the mutation in sperm (green line) and in the soma (brown dot) are shown together with their 95% exact confidence interval. Shared mutations tend to be of higher AF compared to Sperm .

Article Snippet: All putative mosaic mutations and additional control single-nucleotide polymorphisms (SNPs) from the sperm donors were then subjected to validation using massive parallel amplicon sequencing (MPAS, AmpliSeq for Illumina Custom DNA Panel) .

Techniques: Mutagenesis, Biomarker Discovery, Amplification, Sequencing, Variant Assay

Journal: bioRxiv

Article Title: Sperm mosaicism predicts transmission of de novo mutations to human blastocysts

doi: 10.1101/2022.03.28.486034

Figure Lengend Snippet:

Article Snippet: All putative mosaic mutations and additional control single-nucleotide polymorphisms (SNPs) from the sperm donors were then subjected to validation using massive parallel amplicon sequencing (MPAS, AmpliSeq for Illumina Custom DNA Panel) .

Techniques: Amplification, Sequencing