Analyses are disease specific (e.g. biomarkers are matched depending on the cancer type in which they have been reported).

The tumor subtypes structureof the selected disease is taken into account to process the data (e.g. patients with lung adenocarcinoma or squamous cell carcinoma both match with biomarkers described for non-small cell lung cancer)

The file must follow the vcf format specifications (http://samtools.github.io/hts-specs/). Only GRCh37/hg19 coordinates are currently supported.

Note that all the variants in the file will be analysed (regardless of e.g. the QUAL and FILTER columns values). In addition, certain parameters of interest (as the germline and/or tumor origin of the variantsor their allele frequency) cannot be retrieved from the generic format specifications and thus are not included in the report of the public version of the tool.

Variants in HGVS format (http://varnomen.hgvs.org/) for protein, cDNA and genomiccoordinates are accepted. The system will check for their consistency and convert them to unambiguous left-aligned GRCh37/hg19 genomic coordinates. In case that any problem isencountered during that process, the system will raise the corresponding warning and will not proceed with the analysis.

HGVS protein

Use the gene symbol and the protein change (separated by colon ‘:’). Note the required use of the ‘p.’ prefix to flag that the variant is represented in protein nomenclature. See the following examples:

Aminoacid change: NRAS:p.Q61L

Stop codon insertion: PTEN:p.R233*

Inframe insertion: AATK:p.P1331_A1332insTP

Inframe deletion: AADACL4:p.W263_I267delWRDAI

Inframe del plus insertion: TSC1:p.N198_F199delinsI

Frameshift: BRCA1:p.S1330Rfs*5

HGVS cDNA

Use the gene symbol plus the cDNA change (separated by colon ‘:’). Note the required use of the ‘c.’ prefix to flag that the variant is represented in cDNA nomenclature. See the following examples:

Substitution of a nucleotide: CHEK1:c.207A>C

Insertion of a single nucleotide: VHL:c.477_478insC

Insertion of several nucleotides: EGFR:c.2310_2311insGGTACA

Deletion of a single nucleotide: FAM175A:c.908delA

Deletion of several nucleotides: PALB2:c.172_175delTTG

Insertion and deletopm of several nucleotides: MRE11A:c.592_593delGTinsTA

HGVS genomics

Use the gene symbol plus the genomic change (separated by colon ‘:’). Only GRCh37/hg19 coordinates are currently supported. Note the required use of the ‘g.’ prefix to flag that the variant is represented in genomic nomenclature. Note also that the nucleotides must be stated in the ‘+’ strand. See the following examples:

Substitution of a nucleotide: chr3:g.52437215C>T

Insertion of a single nucleotide: chr17:g.37880991_37880992insC

Insertion of several nucleotides: chr3:g.10188243_10188244insAGA

Deletion of a single nucleotide: chr8:g.90965676delT

Deletion of several nucleotides: chr13:g.32903583_32903584delGA

Insertion plus deletion: chr7:g.140453136_140453137delACinsTT