MUTATION TASTER

Presented by:Adeen Farooq (Roll no.16)Hina Qaiser (roll no. 18)

MutationTaster integrates information from different

biomedical databases and uses established analysis tools

(Supplementary Methods).

Analyses comprise evolutionary conservation, splice-site

changes, loss of protein features and changes that might affect the

amount of mRNA.

Test results are then evaluated by a naive Bayes classifier2,

which predicts the disease potential. A typical query is completed

in less than 0.3 seconds.

MUTATION TASTER

Web interface of Mutation Taster application

GeneYou can identify your gene of interest by entering either of the following:- HGNC symbol e.g. LEP (case insensitive)- NCBI GeneID e.g. 3952- Ensembl gene ID

TranscriptYou can also directly enter the Ensembl transcript id (starting with ENST, e.g. ENST00000308868) of your gene of interest.

Position / snippet refers to•Choose coding sequence if you are working with coding sequence positions / sequence for localising the alteration of interest. •Choose transcript (cDNA sequence) if you are working with cDNA positions / sequence for localising the alteration of interest.•Choose gene (genomic sequence) if you are working with gDNA positions / sequence for localising the alteration of interest.

INPUT

Alteration, all types by sequenceChoose all types by sequence if you have a sequence snippet around an alteration that you want to analyse. You can paste this sequence snippet into this field, putting square brackets [ ] around the altered base and the new base (e.g. ACGGTT[A/G]CTCTAAGGA for a base exchange from A to G).

Alteration, single base exchange by positionChoose single base exchange by position if you are working with a single base exchange. This means, that only one single base is altered.

Alteration, insertion or deletion by positionChoose insertion / deletion by position if you are working with an insertion, a deletion or a combination thereof. You do not need to further specify which kind of alteration you are exactly dealing with, since this is automatically determined by the software (and displayed in the output).

OptionsCheck 'show nucleotide alignment' if you want to see multi-species alignment of nucleotide sequence around the submitted alteration in the results.

Name of alterationYou can enter a self-chosen name for the alteration in question. This will be displayed in the output in order to facilitate the identification of printed outputs for different mutations in the same gene.

MODELS: It provide three different models aimed at different types of alterations, either aimed

at 'silent' (non-synonymous or intronic) alterations (without_aae model), at those leading to the substitution/insertion/deletion of a single amino acid (simple_aae model) at more complex changes of the amino acid sequence (e.g. mutations introducing a premature stop codon, etc -complex_aae model).

Output: probability valueThe probability value is the probability of the prediction, i.e. a value close to 1 indicates a high 'security' of the prediction.

•BAYES CLASSIFIER

OUTPUT

PredictionMutationTaster predicts an alteration as one of four possible types:disease causing - i.e. probably deleteriousdisease causing automatic - i.e. known to be deleteriouspolymorphism - i.e. probably harmlesspolymorphism automatic - i.e. known to be harmless

Different elements of output:Summary, name of alteration, alteration (phys. location), HGNC symbol, Ensembl transcript ID, UniProt peptide (SwissProt ID), alteration type, alteration region, DNA changes, AA changes, position(s) of altered AA, frameshift, dbSNP / TGP / ClinVar / HGMD, regulatory features, splice sites, Kozak consensus sequence altered, conservation on AA level, protein features, length of protein, AA sequence altered, position(s) of altered AA, poly(A) signal, cDNA position, chromosomal position, speed.

dbSNP / TGP / ClinVar / HGMDFormatsMutationTaster provides information in either of the following formats:> 4 cases homozygous in TGP: TGP: allele_alt/allele_alt found more than 4 times in TGP data: #homozygous_hits

> 4 cases heterozygous in TGP: TGP: allele_ref/allele_alt found more than 4 times in TGP data: #heterozygous_hits (#homozygous_hits for allele_alt/allele_alt)

< 4 cases homo-/heterozygous in TGP: TGP: allele_ref/allele_alt found #heterozygous_hits times in TGP data, allele_alt/allele_alt #homozygous_hits times.

phyloP / phastConsphastCons and phyloP are both methods to determine the grade of conservation of a given nucleotide.

phastCons values vary between 0 and 1 and reflect the probability that each nucleotide belongs to a conserved element, based on the multiple alignment of genome sequences of 46 different species (the closer the value is to 1, the more probable the nucleotide is conserved). It considers not just each individual alignment column, but also its flanking columns.

By contrast, phyloP (values between -14 and +6) separately measures conservation at individual columns, ignoring the effects of their neighbors. Moreover, phyloP can not only measure conservation (slower evolution than expected under neutral drift) but also acceleration (faster than expected). Sites predicted to be conserved are assigned positive scores, while sites predicted to be fast-evolving are assigned negative scores.

Disease mutation via sequence snippetSOD1_H47R: Imagine a patient suffering from ALS. You decide to sequence the exons of

the SOD1 gene. By looking at the sequence reads, you find an A->G point mutation. The sequence after this exchange is TGTTCATGAGTTTGGAGATAATACAGCAGGCTGT.

Polymorphism via gene positionAGRN_g._6052_6053delTTImagine a patient with a muscular disease. Among others, you sequence the complete sequence of the agrin (AGRN) gene and find a deletion of 2 bases: TT at position 6052 and 6053. Is this likely to be disease-causing, e.g. by destroying the reading frame?

DISEASE MUTATION VIA CHROMOSOMAL POSITION

CHRND_L63PImagine you sequenced the complete exome of a patient suffering from Myasthenic syndrome. You find a mutation in the gene for the delta subunit of the nicotinic acetylchloline receptor on chromosome 2 (chr2:233391374t>c).

Whole exome/genome sequencing: complete genotypes

Imagine you sequenced a complete genome of a patient with Myasthenic syndrome. Amanzingly, you end up with just 5 alterations.

EXAMPLE OF SINGLE BASE ALTERATION BY POSITION