Genetics Vocabulary

Question 1

Chromatin

Answer 1

Material composing chromosomes; packages DNA into dense structures.

Question 2

Coverage

Answer 2

Percentage of the genome that has been sequenced at N depth. This number is used to ensure the region has been covered. Expressed as a percentage — 95% coverage means 95% of the region has been sequenced at least once

Question 3

Depth

Answer 3

Number of times a specific base is read during sequencing. A higher depth provides more confidence. If sequenced 20 times, sequencing depth is 20X.

Question 4

Flow cell

Answer 4

Glass slide with lanes, with billions of nanowells in an array. Each nanowell is coated in 2 kinds of oligos complementary to adaptor region; monoclonal clusters form in these nanowells during bridge amplification. The flow cell is loaded into the sequencer after library prep.

Question 5

Hapten

Answer 5

Small molecules that can combine with a specific antibody, but lack antigenicity of their own.

Question 6

Locus

Answer 6

Location in the chromosome where a particular gene is located.

Question 7

Read

Answer 7

A “read” is an oligonucleotide that’s been sequenced.

Question 8

RIN/DIN

Answer 8

RNA Integrity number and DNA integrity number. Highly intact = 10, degraded = 1.

Question 9

Read count

Answer 9

Number of oligonucleotides that have been sequenced.

Question 10

Low pass sequencing

Answer 10

A technique in which each base in the entire genome is sequenced just a few times (known as low-depth coverage). Typically, depth is below 5X and can be as low as 0.1-1 times.

Question 11

karyotype

Answer 11

An individual’s complete set of chromosomes. The term also refers to a laboratory-produced image of a person’s chromosomes isolated from an individual cell and arranged in numerical order.

Question 12

transcriptomics

Answer 12

The analysis of the RNA transcripts produced by the genotype at a given times. Links the genome, the proteome, and the cellular phenotype.

Question 13

Maternal haplogroup

Answer 13

A family of mitochondrial DNA (mtDNA) that traces back to a single common ancestor.

Question 14

SVs

Answer 14

Structural variations, or large genomic alterations of 50bp or larger. Includes deletions, duplications, insertions, inversions, and translocations; as well as CNVs.

Question 15

Short-read sequencing

Answer 15

Short-read technologies sequence by synthesis or ligation. Each strategy uses DNA polymerase or ligase enzymes, respectively, to extend numerous short DNA strands in parallel. Includes NGS sequencing.

Question 16

Long-read sequencing

Answer 16

Long-read sequencing sequences 5K-30K base pairs. Eliminates amplification bias (only uses 1 molecule), and generates a reasonable length to overlap a sequence for better sequence assembly. Long-read sequencing allows the detection of complex, large SVs.

Question 17

Fusion gene

Answer 17

Hybrid genes formed when two previously independent genes become juxtaposed. The fusion can result from structural rearrangements, transcription read-through of neighboring genes, or the trans- and cis-splicing of pre-mRNAs.

Question 18

Aneuploidy

Answer 18

The occurrence of one or more extra or missing chromosomes in a cell or organism. Humans should have 23 haploid chromosomes.

Question 19

Isoforms

Answer 19

Functionally similar proteins that have a similar but not identical amino acid sequence. Encoded by different genes or by RNA transcripts from the same gene which have had different exons removed.

Question 20

Allele-specific expression

Answer 20

A phenomenon in which one allele is preferentially expressed over the other.

Question 21

Paired-end read

Answer 21

Sequencing that starts at one end, finishes that direction at the specified read length, and then starts another round of reading from the opposite end of the fragment. Generates high-quality, alignable sequence data. Facilitates detection of genomic rearrangements and repetitive sequence elements, as well as gene fusions and novel transcripts.

Question 22

Single-end read

Answer 22

Single-read sequencing involves sequencing DNA from only one end. More cost effective, can be a good choice for certain methods such as small RNA-Seq or chromatin immunoprecipitation sequencing (ChIP-Seq).

Question 23

Neoantigen

Answer 23

Newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response.

Question 24

Neoepitope

Answer 24

An epitope the immune system has not encountered before. Not subject to tolerance mechanisms of the immune system. As the mutant gene product is only expressed in tumors and is not found in non-cancerous cells, neoepitopes may evoke a vigorous T cell response.

Question 25

Germline NGS

Answer 25

Sequencing for hereditary mutations in sex cells. NGS can detect large numbers of germline mutations at once and/or identify novel germline variants linked to cancer.

Question 26

Somatic NGS

Answer 26

Sequencing for mutations that occurs in any of the cells of the body, except the germ cells. Somatic mutations often indicate cancer.

Question 27

CAR-T therapies

Answer 27

CAR T-cell therapies are customized for each individual patient. They are made by collecting T cells from the patient and re-engineering them in the laboratory to produce chimeric antigen receptors (CARs). CARs recognize and bind to specific Ag on the surface of cancer cells. 6 FDA approved therapies for blood cancers are available, and though they're becoming SOC, their hefty price tag ($450K) is a barrier.

Question 28

IO adjuvant therapies

Answer 28

Additional immune/oncology therapies given after primary cancer treatment to lower the risk that the cancer will come back.

Question 29

QNS rates

Answer 29

Quantity not sufficient (QNS) rate

Question 30

Neoplasm

Answer 30

A new and abnormal growth of tissue in some part of the body, especially as a characteristic of cancer.

Question 31

Microsatellite instability

Answer 31

A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellite instability (MSI) is the condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR). Also called mismatch repair deficiency.