Data analysis pipeline

The iBinom pipeline improves analysis through precision, sensitivity and specificity. This is accomplished by quality control and efficient algorithms finely tuned by our team.

Works with any of the most popular sequencing instrument specification. We guarantee reproducible and ultimately accurate results.

Percentage of low quality and mapped reads	Average length of reads and depth of coverage	SAMtools variant caller v. 1.2	BWA-MEM aligner v. 0.7.8	Regular GC content

iBinom variant filtration tool

The iBinom filtration system is intuitive and flexible. It shortens the path to detecting the causative variants. Databases are always up-to-date. Files can be re-analysed whenever needed.

Genes and variants

Filter by gene name, coordinates, rsID

Diseases

Search by internal disease database and ACMG incidental findings list

Data quality

Apply thresholds for VCF coverage depth and calling quality

Variant information

Filter by effect, zygosity and variant type

Population frequency

Filter by frequencies for different cohorts from ExAC, 1000GP3, TwinsUK, ESP6500, ALSPAC

Pathogenicity and conservation scores

Filter by SIFT, polyphen2, mutationtaster, FATHMM and other scores

Variant report

The report shows the most credible variants discovered from the last filtering step. No more endless candidate variants to consider.

The report is designed according to the ACMG's recommendations

Scores

Show pathogenicity by deviation to the right on the strip.

Frequencies

Show low mutation frequency by lowering the slope on the graph.

Database and filtering list

Variant effect

Intergenic, Intragenic

Exon Deleted

Synonymous coding, vstart, stop

Non synonymous coding, start

Downstream

Frame shift

Transcript

Upstream

Utr 3, 5

Start lost, stop gained, stop lost

Splice site acceptor, donor

Codon

Intron

Pathogenicity scores

SIFT, ensembl 66, 15’ jan

MutationAssessor, v2, 13’ sep

MutationTaster, v2, 14’ jul

Phastcons7way vertebrate, 14’ jun

Phylop7way vertebrate, 14’ jun

PolyPhen hvar, v 2.2.2, 12’ feb

Fathmm, v2.3, 14’ nov

SiPhy 29way, 11’ may

GERP++ , 11’ may

Population frequency

UK10K (TwinsUK and ALSPAC), 14’ jun

1000 Genomes, phase 3, 15’ feb

ESP6500, 14’ nov

ExAC v0.3, dec’ 14

Disease databases

Manually curated databases

dbSNP build 144, 15’ jun

Clinvar, 15’ sep

dbNSFP, v3.0, 15’ aug

Sequencing quality

Strand bias

BaseQ bias

MapQ bias

End distance bias

Variant quality

Depth

Variant type and localization

SNP, DEL, INS

Homozygote, heterozygote

Chromosome position

Autosomal, sex

dbSNP id

Team

The core team has versatile competencies, education and experience which comprises biotech companies' management and growth, molecular biology and bioinformatics deep knowledge, algorithms and IT strong expertise along with international business skills.