Genome Sequencing Information and Education

This site is your starting point for preparation towards undertaking medical DNA testing. Thorough review of the following content will ensure proper preparation towards your informed consent to pursue DNA testing.

Step 1: Educate yourself

Glossary

Actionable variant – a mutation that is either pathogenic or likely to be pathogenic, and for which intervention can be undertaken.

Allele – a gene or DNA sequence (locus) that has an alternative form (through altered sequence). Alleles can produce observed variations of a trait (phenotype). Trait differences that arise due to differences in the same gene (or locus) are referred to as allelic. Trait variations that arise from different genes or different loci are referred to as nonallelic.

Annotation – commentary that provides insight into the function of a DNA sequence (such as what gene it represents, the architecture of the gene it represents, the amino acid sequence of the protein coded for by the gene).

Autosomal dominant variant – an autosomal variant that results in specific trait development when inherited from a single parent.

Autosomal recessive variant – an autosomal variant that results in specific trait development only when inherited from both parents.

Call – assignment of a nucleotide base (A, T, G, C) to a specific position in a DNA sequence during sequencing.

Carrier – person who carries a single copy of a genetic variant known to contribute to a disorder inherited in a recessive fashion. Recessive diseases can be developed only if two copies of the mutant allele are present in the genome. Carriers do not display the disorder but can pass on the genetic variant to their offspring. An offspring who inherits a copy of the variant from each parent will develop the disorder. The chance of two carriers having a child with the disorder is 25%.

Causative variant – a variant that has been established to lead to a specific trait, including disease.

Coverage (sequencing coverage, coverage depth) – the number of independent times a DNA segment (typically a fragment of a specific genome location) is sequenced. The higher the coverage, the higher the accuracy of the nucleotides being called correctly in that DNA sequence.

Curation – manual review of available scientific information (published literature, databases, use of predictive modeling programs, or other qualified data sources) to help determine whether a specific variant could be pathogenic or benign.

Direct-to-consumer genomic services – services outside of medical or academic oversight. This means the decision making resides with the consumer, not with another individual or an institution. It also means the procedure is not bound by the regulations that bind medical or learning institutions.

DNA sequencing – method for determining the nature and order of nucleotides present in a DNA sequence.

Exome – the entire protein-coding portion of the genome.

Gene – DNA sequence that codes for protein production. Only about 1–2% of the human genome codes for expressed proteins.

Genome – the entire DNA sequence in an organism.

Genomic counseling – informative session provided by a professionally accredited genetic counselor to an individual who is considering or who has undergone genome sequencing. The session aims to educate a prospective client with regard to potential psychosocial impacts of genomic testing and the significance of informed consent for genomic testing. It explains genome based disease risk assessments, their medical and familial implications, and some ways in which these implications can be managed. Genomic counseling can differ substantially from traditional genetic counseling in that genomic counseling emphasises the entire genome, whereas genetic counseling emphasises individual genes.

Genomic medicine – medical management of an individual based on knowledge of the individual’s genome; examples include screening for disease conditions, diagnosis of disease, disease treatment choice, or counseling.

Genotyping – genome-wide probe for previously discovered single nucleotide variants.

Germline variant – a variant present in the genome from the moment of fertilization and passed on through cell division to every cell in the body.

Haplotype – a group of variants in the same section of a genome that are inherited together as a group.

Incidental findings – unexpected positive findings, however, in context of genomics it can refer to actively sought pathogenic or likely pathogenic DNA alterations beyond reasons for which the sequencing test was ordered.

Locus (plural loci) – the physical location of a gene or other identifiable DNA sequence on a chromosome.

Next generation sequencing – a new method of sequencing DNA that allows for analysis of millions of DNA fragments at the same time (high-throughput) at much lower cost and more rapid pace than the traditional sequencing method of one DNA strand at a time. Due to the ability of sequencing millions of DNA segments simultaneously, this technology is also sometimes referred to as massively parallel sequencing.

Pathogenic variant – a genetic mutation with a direct consequence to human health. A pathogenic variant can be considered “actionable” if the condition resulting from the pathogenic mutation is treatable or “nonactionable” if the condition resulting from the pathogenic mutation is untreatable.

Penetrance – the extent to which a disease will be manifested.

Personalized medicine – health care strategies tailored to treat a single individual.

Pharmacogenomics – study of correlations between variations observed in a human DNA sequence and drug efficacy or risk of adverse events related to drug use. Specific variants in an individual’s genome can point to how that individual might respond to a specific medication.

Phenotype – physiological trait; observable or measurable biological attribute.

Sex chromosome variant – a variant present on the X or Y chromosome.

SNP – single nucleotide polymorphism; observed variation of a single nucleotide among a population in a specific DNA location. SNPs can lead to variations in observed traits.

Somatic variant – a spontaneous mutation that was not inherited from parents. Such mutations can appear in the genome of any cell in the body at any time during a person’s lifespan. Some somatic mutations can affect cell cycle regulation leading to cancerous phenotype.

Structural variant – a type of variant that involves alteration of a large segment of DNA; examples are duplications, deletions, inversions, and transfer to a different genomic location.

Variant (previously mutation or polymorphism) – a DNA sequence that varies from the sequence commonly found in the population; variants can involve one (most common) or more than one nucleotide.

Whole exome sequencing – detection of the nature and precise order of nucleotides in the entire protein-coding portion of the genome (termed exome).

Whole genome sequencing – detection of the nature and precise order of nucleotides in the genome, or the entire DNA content in an organism. In humans, certain sections of the genome (for example, DNA consisting of many repeat fragments) may not be sequenced with standard methods, therefore, components of the genome might be absent in a present-day whole genome sequence.

Zygosity – an inheritance configuration typically denoted for a specific DNA site which is linked to a condition of interest but also used to describe the inheritance pattern of the condition itself.