Reference Guide 

A complete list of gene description with health conditions – click to view the complete guide.

DNA 

A DNA or deoxyribonucleic acid is a molecule that encodes genetic information for the development and functioning of living organisms. DNA is composed of chains of subunits that are called nucleotides (also called “bases”).  There are four nucleotides: adenine (A), cytosine (C), thymine (T) and guanine (G). The specific order of these nucleotides in a DNA molecule is the DNA sequence and encodes the genetic information, much how the specific order of letters in a word conveys information to readers.

Genome

A genome is the entire set of genetic material for an organism. The human genome consists of about 3 billion base pairs of DNA across 23 pairs of chromosomes, which are present in two copies in both men and women. While most cells in our body have two copies of each chromosome, sperm and eggs carry only one copy of each chromosome. When a sperm fertilizes an egg, the embryo now contains two copies of each chromosome, one from the father and one from the mother. Consequently, each person has two copies of every gene carried on a chromosome: one inherited from their father and one from their mother. More than 99 percent of the human genome is the same in all people. That means that differences, also known as variants, in less than 1 percent of our genome accounts for the vast diversity of humans across the globe.

Genes

Most genes encode proteins, which are a group of complex molecules that perform critical roles in our cells and bodies. The current estimate is that the human genome, which is all the DNA sequences in our cells contains approximately 25,000 genes.

DNA sequencing

DNA sequencing identifies an individual’s variants by comparing the DNA sequence of an individual to the DNA sequence of a reference genome maintained by the Genome Reference Consortium (GRC). There are different ways that one person’s DNA sequence can differ from the reference   DNA sequence, some of which are:

• Deletions are when there are missing nucleotides, relative to the reference sequence.
• Substitutions are when multiple nucleotides are altered from the reference sequence.
• Single nucleotide polymorphisms (“SNPs”, pronounced “snips”) are DNA sequence variations that occur when a single nucleotide differs from the reference DNA sequence.
• Insertions are when additional nucleotides inserted in a DNA sequence, relative to the reference sequence.
• Structural variants are changes where large sections of a chromosome or even whole chromosomes are duplicated, deleted or rearranged in some manner.

Variants and Variation

The average person’s genome has millions of variants. Some variants occur in genes but most occur in DNA sequences outside of genes. A small number of variants have been linked with diseases, but most variants have unknown effects. Some variants contribute to the differences between humans, such as different eye colors and blood types.

Classification of Variant types:

The American College of Medical Genetics and Genomics (ACMG) has developed guidelines for the classification of DNA sequence variants:

• Pathogenic and likely Pathogenic (VLP) is a genetic alteration that increases an individual’s susceptibility or predisposition to a certain disease or disorder and has been previously reported and recognized to have a high association with the disorder.
• VUS (Variant of Unknown Significance) is a variant form of a gene, which has been identified through genetic testing, but whose significance to the function or health of an organism is not known.
• Likely Benign (VLB) is a sequence variant for which there is strong evidence against pathogenicity.
• Benign is a sequence variant for which there is very strong evidence against pathogenicity. Benign alterations are not routinely included in results reports.

Understanding the effects of variants is a very complicated process. While there are many publicly available sources of information about variants and their classification based on ACMG guidelines that link variants to diseases, knowledge about variants is constantly evolving and inconsistencies and inaccuracies can be found in these sources.  Any health-related matters should be directed to your doctor or another qualified medical professional.

References:

Alberts, B., et al (2008). Molecular biology of the cell. New York,  NY: Garland Science; Hartl, D.L.  Jones, E.W.  (2005).  Genetics: analysis of genes and genomes.   Sudbury,  MA: Jones and Bartlett  Publishers.  Pesaran T, et al.  Beyond DNA:  An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes.  Int  J Breast Cancer. 2016;2016:2469523.

Richards S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.  Genet Med. 2015  May;17(5):405-24. Caleshu  C, et al. Use and interpretation of genetic tests in cardiovascular genetics.  Heart. 2010  Oct;96(20):1669-75.  Plon SE, et al.  Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum    Mutat. 2008 Nov;29(11):1282-91.