Sequencing Use Cases Flashcards
Why, how and when different analyses in Fulgent's portfolio are used.
What are some advantages and disadvantages of whole genome sequencing (WGS)?
WGS is 2-3 times more expensive than WES. This is due to the volume of information produced, which requires more storage space, computing power and analysis time. WGS is more comprehensive than WES and has less bias, as it does not include PCR or target enrichment (and thus has a uniform read depth).
What are some advantages and disadvantages of whole exome sequencing (WES)?
WES is much lower-cost than WGS, as it only focuses on coding regions (exons), about 2-5% of the genome. However, it is not validated for the detection of SVs such as CNV, inversions and translocations; and does not cover interons, which can regulate gene expression.
What can methylation sequencing reveal?
DNA methylation reveals epigenetic modification, which is essential for many physiological and pathological processes, such as the development of cancer.
Why do we sequence mitochondrial DNA (mtDNA)?
mtDNA resists degradation and has a high copy number inside the cell. It is recoverable when nuclear DNA may be sparse or degraded. It can also be used to trace matrilineal ancestry and human evolution, due to its maternal inheritance and lack of recombination.
Why do we use Sanger sequencing still today?
Sanger sequencing is highly accurate and the “gold standard” of sequencing. It is used to validate gene variants identified via NGS. Best for analyzing small numbers of gene targets on a deadline.
How do DNA liquid biopsy molecular profiles help oncologists?
They enable precision oncology via identifying and monitoring of genetic mutations in ctDNA, cfDNA and CTCs. They can help assess treatment response and identify resistance to therapy.
Why perform a DNA & RNA solid tumor molecular profile?
A solid biopsy details mutations found within an area of an individual tumor, which provides better specificity than a liquid biopsy. Analyzing both DNA and RNA allows for better detection of fusion genes.
What are some applications of HLA typing?
HLA typing can be used to match transplant donor to recipient and diagnose ankylosing spondylitis. HLA typing of a family can indicate paternity and risk of diseases such as hematochromatosis and juvenile-onset diabetes mellitus.
Why perform a DNA and RNA heme NGS panel?
Heme NGS panels are used to detect mutations associated with hematologic myeloid and lymphoid disorders. Using DNA and RNA allows for better detection of fusion genes and optimal sensitivity.
What is the purpose and limitations of pharmacogenetics (PGx) testing?
PGx aims to guide personalized treatment strategies that improve therapeutic outcomes, optimize the medication selection process. However, relationship between genotype and drug response is not well understood for all drugs.
What advantages does RNASeq have over other RNA sequencing methods like qPCR?
RNASeq doesn’t require primers or probes, which limits bias and allows for discovery. This broad picture provides insight into which genes are active, their level of transcription, and when they’re activated or shut off.
What is the purpose of mRNA sequencing?
mRNASeq provides a clear picture of the transcriptome. It can quantify gene expression, identify known and novel isoforms in the coding transcriptome, detect gene fusions, and measure allele-specific expression.
Why conduct a microarray analysis?
To identify SNPs and infer levels of gene expression. Microarray is also used to investigate chromosomal deletions, duplications and aneuploidies through chromosomal microarray analysis.
Name some use cases of a FISH analysis.
FISH can be used to visualize large-scale gene mutations in cancer; chromosomal abnormalities before or after birth; chromosomal abnormalities in an embryo during preimplantation genetic testing as a part of IVF (in vitro fertilization).
What is the most common application of cytogenetics?
Cytogenetics is often used to karyotype – to efficiently analyze the entire chromosome set for numerical and structural abnormalities.
When might you perform qPCR instead of another genetic analysis?
qPCR is typically a good choice when the number of target regions is low (≤ 20 targets) and when the study aims are limited to screening or identification of known variants. This smaller scope can be more cost effective.
