NGS technology of family trio analysis offers a powerful approach for identifying causal variations for inherited diseases. Trio analysis can identify variants inherited from the parents. For example, if a variant appears only in the mother, and the father and child do not carry that variant, it is called a maternal variant. The most important inheritance type in this analysis is de novo variant. If the variant occurs in the offspring but is not present in either of the parent, it is termed as a de novo variant. The possibility of pathogenicity of de novo variations is generally high. ACMG guideline has two criteria for this. One of them is PM6 and the other one is PS2. PS2 criterion is used if the parents prove that they are the biological parents of the child but PM6 does not need that confirmation, because of that while PS2 represents strong pathogenicity, PM6 represents moderate.
When entering the data, the user must indicate to the system which sample belongs to whom. This information will be considered confirmation for PS2 ACMG criteria by Massive Analyser.
Result output
- Uploaded Variation
- rs ID
- Gene Symbol
- Var. Class
- Consequence
- Mother GT – Mother zygosity
- Father GT – Father zygosity
- Child GT – Child zygosity
- Inheritance
- ACMG criterias
- Pathogenicity classification
- Details1 – It includes exon, nomenclature for protein and sequences (HGVS), canonicality situation,impact and etc.
- SIFT in silico pathogenicity prediction tool
- SIFT4G in silico pathogenicity prediction tool
- PolyPhen in silico pathogenicity prediction tool
- MetaLR in silico pathogenicity prediction tool
- REVEL in silico pathogenicity prediction tool
- MutationTaster in silico pathogenicity prediction tool
- MutationAssessor in silico pathogenicity prediction tool
- PROVEAN in silico pathogenicity prediction tool
- FATHMM in silico pathogenicity prediction tool
- Condel in silico pathogenicity prediction tool
- DEOGEN2 in silico pathogenicity prediction tool
- LRT in silico pathogenicity prediction tool
- RF score in silico pathogenicity prediction tool
- ADA score in silico pathogenicity prediction tool
- Eigen-raw coding in silico pathogenicity prediction tool
- DANN score in silico pathogenicity prediction tool
- LoFtool in silico pathogenicity prediction tool
- GeneSplicer, detect splice cite in genomic regions
- The Exome Aggregation Consortium (ExAC) Total allele frequency and subpopulation frequency
- 1000Genomes Total allele frequency and subpopulation frequency
- NHLBI-Exome Sequencing Project (ESP) subpopulation frequency
- gnomAD Total allele frequency and subpopulation frequency
- MAX AF -Maximum observed allele frequency in 1000Genomes, ESP and gnomAD
- phastCons100way conservation score in vertebrates
- phastCons17way conservation score in primates
- phastCons30way conservation score in mammalians
- phyloP100way conservation score in vertebrates
- phyloP17way conservation score in primate
- phyloP30way conservation score in mammalian
- GERP++ RS conservation score
- BLOSUM62 conservation score
- ClinVar CLNSIG clinvar variant pathogenicity result
- ClinVar CLNSIGCONF- Conflicting clinical significance for variants
- ClinVar CLNREVSTAT- ClinVar review status for the Variation ID
- ClinVar gold stars- Stars provide a graphical representation of the aggregate review status
- Phenotype information
- UniProt accession link
- HGNC accession link
- ClinVar accession link
- dbSNP accession link
- Varsome accession link
- Sequence Ontology accession link
- GeneCards database accession link
- UCSC Genome Browser accession link
- OMIM accesion link
- HP accession link
- MONDO acccession link
- PubMed-Phenotype paper link
Inheritance table involves the variant inheritance type (maternal, de novo and etc.). The table below explain inheritance of variants in detail.
