Glossary and Terms Used in Genomics

Actionable mutation

An actionable mutation is a gene mutation that has a specific target that can be acted upon by a drug therapy. Not all gene mutations have targets; however, Intermountain Precision Genomics is successful about 80% of the time in matching a person to a drug treatment. Benign: If a tumor does not contain cancerous cells it is referred to as benign.

Analytical metrics

Used for determining adequacy of the bioinformatics pipeline for analysis of target regions include ability to align, map, or assemble reads and call variants.

Bioinformatics

The science of collecting and analyzing complex biological data such as genetic codes.

Biomarkers

Short for biological markers, biomarkers are characteristics that show normal or expected biological behavior, specifically in how the body responds to therapies and treatments.

Biorepositiory

An area dedicated to collecting, processing, storing, and distributing biological materials and specimens to support future scientific investigation Biorepositories can contain or manage specimens from animals, including humans, and many other living organisms.

Cancer pathways

Neurological connections that alter and form cancerous tumors.

Chemotherapy

The treatment of disease by the use of chemical substances, especially the treatment of cancer by cytotoxic and other drugs.

Criteria for variant calling

Covers minimum read coverage depth, base or variant quality scores, Allelic read percentage.

Depth of coverage

At Intermountain Precision Genomics we have found a way to more thoroughly analyze a patient’s genes by increasing the depth of a tissue sample.

DNA

The material that carries our genetic information, DNA stands for deoxyribonucleic acid Gene: A unit of the body that carries our characteristics and can be passed from parents to children.

Genetic makeup

The unique combination and order of our genes/DNA that determine characteristics like the color of our eyes and the size of our feet.

Genetic mutation

A permanent alteration in our DNA that causes it to behave and replicate differently, and in some cases can result in tumors forming. Genetic sequence: The order of our genes/DNA, which can impact our characteristics.

Hotspot mutation region

Covers only the region of interest where mutations are observed with higher frequency.

ICG100™ test

Intermountain Precision Genomics ICG100™ offers a targeted cancer panel that detects 96 genomic alterations commonly associated with solid tumors. The assay looks at whole-exome sequencing (WES) instead of just a hotspot mutation region.

Malignant

If a tumor does contain cancerous cells it may be referred to as malignant.

Mean depth coverage

The average coverage of all exons across patient samples (n=60) sequenced in Intermountain Cancer Genomics lab.

Molecular Tumor Board

Exclusive to Intermountain, the Molecular Tumor Board, or MTB, is a group of physicians and experts specialized in cancer and genetics.

Oncologist

A physician who specializes in treating cancer.

Pathologist

A physician who interprets and diagnoses the changes caused by disease in tissues and body fluids.

Radiology

The science dealing with X-rays and other high-energy radiation, especially the use of such radiation for the diagnosis and treatment of cancer.

Tissue sample

Physicians remove a small piece of a tumor so that we can test it, analyze it, and determine if it contains cancer.

Tumor

An abnormal mass of tissue that may or may not contain cancerous cells.

Tumor profiling

The process of examining the genetic makeup of a tumor and determining what type of cancer may be present. Wet lab: A laboratory that examines tissue samples.

Validation process

Follows the entire "beginning to end" bioinformatics pipeline (e.g. read alignment, mapping or assembly, variant calling).

Quality threshold

The quality threshold is the percentage of exons that are covered at 10X or higher.

WES

Whole exome sequencing covers all the functionally important protein coding genes in a genome that entail biologically important DNA sequences (exons).