X-linked intellectual disabilities

Methodology

Information on the test method:

At first, deoxyribonucleic acid (DNA) is isolated from a blood sample or paraffin embedded tissue block. The quantity and quality of the material is determined in spectrophotometric and fluorometric assays. From mechanically or enzymatically fragmented DNA a library is made to be used for determination, sequencing and examination of selected genes. The library is sequenced on a new generation sequencer. Afterwards, sequencing results are subjected to bioinformatics analysis and clinical interpretation. Genetic variants are identified using BurrowsWheeler Aligner. The test detects 100% of substitutions and 95% of small insertions and deletions.

Information on variant classification:

The study report provides information on variants classified as ‘potentially pathogenic’ and ‘pathogenic’ depending on their suspected clinical significance. The identified variants are classified under the following categories:

Pathogenic variant: the detected change in the gene sequence directly associates with disease development. At the same time, some pathogenic changes may not have full penetration, meaning that a single mutation may not be enough to cause a full-blown disease.

Potentially pathogenic variant: the detected change in the gene sequence may be, with a great probability, associated with disease development however it is not possible to prove this association on the basis of currently available scientific data. Variant pathogenicity confirmation would require additional tests and evidence; it cannot be excluded that further tests might prove that the change has limited or no clinical significance.

Variant of unknown pathogenicity: based on the currently available scientific data it is not possible to determine the significance of the detected change.

Potentially benign variant: the detected change in the gene sequence most probably does not associate with disease development, however based on the currently available scientific data the benignity of the mutation cannot be confirmed. Confirmation of the clinical significance of the variant would require additional tests and evidence; it cannot be excluded that further tests might prove that the detected mutation has clinical significance and would cause disease development.

Benign variant: the detected change does not associate with disease development.

The identified genetic variants are classified based on the guidelines of the American College of Medical Genetics and Genomics and the American Association for Molecular Pathology (S. Richards, Genet Med. 2015 May; 17(5):405-24). In variant classification the following criteria are considered:

• Previous variant identification in persons burdened with the disease
• Variant impact of functional gene product synthesis determined through bioinformatics analyses, confirmed by in vitro/in vivo studies
• Variant location (exon/intron, functional domain)
• De novo/hereditary change
• Variant incidence in general population (each variant with incidence >5% in line with Exome Sequencing Project, 1000 Genomes Project or Exome Aggregation Consortium is classified as benign change)

Variant incidence in general population with relation to patient population The final classification of variants is made on the basis of the total of the above-mentioned criteria. The data bases include: 1000GP, ClinVar, ConsensusPathDB, Exome Aggregation Consortium, Exome Variant Server, FATHMM, GO (Gene Ontology), GTEx (Genotype-Tissue Expression), GWAS (Genome Wide Association Study), HGMD, KEGG, MetaLR, MetaSVM, MutationAssessor, MutationTaster, OMIM, PolyPhen-2, PROVEAN, SIFT, SnpEff, dbNSFP, UniProt, VEP (Variant Effect Predictor).

Test limitations:

All sequencing technologies have some limitations. Our tests use new generation sequencing (NGS) to examine coding and splicing regions of disease-associated genes. Sequencing techniques and subsequent bioinformatics analyses are aimed at limiting the significance of pseudo-gene sequences, however presence of highly homologous gene sequences may still occasionally disturb the identification of pathogenic alleles, deletions/duplications. The Sanger sequencing method is used to confirm variants with lower quality parameters. Deletion/duplication analyses show qualitative changes in DNA covering at least one exon and always require confirmation with other methods (qPCR or MLPA). The analyses are not designed for detecting certain types of genomic changes, such as translocations, inversions, dynamic mutations (e.g. increased number of trinucleotide repetitions) or mutations in regulatory or intronic regions. In case increased numbers of di- or trinucleotide repetitions are reported, it should be assumed that the exact number of repetitions is not precise. The test is not intended to detect somatic mosaicism and somatic mutation analyses should be made in the context of the germinal DNA sequence.

It is not possible to exclude mutations in genes and regions other than those covered by the test as well as alternations in the gene copy number. The test report includes information on changes in gene sequence identified on the basis of a comparison against current reference sequences maintained in NCBI Nucleotide and Ensembl databases. Tests are developed by Warsaw Genomics for clinical objectives. All test results collected are interpreted and analysed by scientific and medical experts of Warsaw Genomics.