Misc Deck (2) Flashcards

Question

What type of DNA is the focus of the Twist Liquid Biopsy workflow?

Answer 1

Cell-free DNA (cfDNA).

Answer 2

Blood should be processed within 48-72 hours.

Answer 3

Low cfDNA input can limit downstream analysis.

Answer 4

Prepares sequencing libraries from extracted cfDNA.

Answer 5

They tag individual DNA molecules to reduce PCR duplicates and improve variant detection accuracy.

Answer 6

To focus sequencing on specific cancer-related regions.

Answer 7

<0.1% VAF.

Answer 8

NGS platform (e.g., Illumina).

Answer 9

Depth and coverage of sequencing.

Answer 10

Process sequencing data and identify tumor-specific mutations.

Answer 11

Treatment escalation.

Answer 12

Detects ctDNA at ≤0.1% VAF.

Answer 13

Works with as little as 1 ng of cfDNA.

Answer 14

Under 2.5 hours.

Answer 15

They ensure the detection of real tumor DNA, not artifacts.

Answer 16

A benchmark to validate assay performance.

Answer 17

It depends on ctDNA shedding rates, which vary by cancer type and stage.

Answer 18

Lack of universal clinical guidelines.

Answer 19

Pairing with high-depth sequencing and robust bioinformatics maximizes MRD detection.

Answer 20

Prepares high-quality NGS libraries from cfDNA extracted from blood, urine, or cerebrospinal fluid (CSF) ## Footnote Enables non-invasive cancer profiling, early detection, and MRD monitoring.

Answer 21

1 ng of cfDNA ## Footnote This is optimized to minimize loss of already scarce cfDNA.

Answer 22

Creates blunt-ended DNA fragments ## Footnote This step is critical for preparing the DNA for subsequent adapter ligation.

Answer 23

Tag individual DNA molecules to reduce PCR duplicates and improve variant detection accuracy ## Footnote Ensures high conversion rates during adapter ligation.

Answer 24

Sequencing both DNA strands to validate findings and minimize false positives ## Footnote Important for maintaining accuracy in detecting rare variants.

Answer 25

Produces sequence-ready libraries in under 2 hours ## Footnote Compatible with Illumina platforms.

Answer 26

Enables MRD monitoring and early cancer screening ## Footnote Critical for tumor profiling without invasive biopsies.

Answer 27

User-designed target enrichment panels for NGS focused on specific genes or regions ## Footnote Examples include cancer-related genes like TP53 and KRAS.

Answer 28

Delivered in 4 weeks ## Footnote This enables rapid research iteration.

Answer 29

NGS tools for cancer research, covering discovery, therapeutic development, and detection ## Footnote Integrates various Twist products to support the cancer research pipeline.

Answer 30

Analyzes ctDNA in body fluids for non-invasive cancer detection ## Footnote Supports early detection, MRD monitoring, and tumor evolution tracking.

Answer 31

DNA methylation, including enzymatic library prep and panels for cancer types ## Footnote Helps identify methylation biomarkers for early cancer detection.

Answer 32

Whole-transcriptome or targeted RNA-seq, detecting low-expressing transcripts and isoforms ## Footnote Supports precision oncology by profiling tumor transcriptomes.

Answer 33

Pre-designed target enrichment covering broad genomic regions or cancer-specific genes ## Footnote Supports large cohort studies and diagnostics.

Answer 34

High-throughput library construction for whole-genome sequencing ## Footnote Processes up to 960 samples per kit.

Answer 35

Provides standardized controls with known ctDNA variants to validate NGS assays ## Footnote Ensures accuracy in liquid biopsy and cancer research.

Answer 36

Normalization by Ligation (NBL) technology ## Footnote Supports ultra-high throughput sequencing for up to 1,152 samples.

Answer 37

True ## Footnote This feature helps to reduce false positives.

Answer 38

[liquid biopsy applications in oncology]

Answer 39

Definition: “Low input” refers to the small amount of starting nucleic acid (DNA or RNA) used for NGS library preparation, typically measured in nanograms (ng) or picograms (pg). 1 ng is equivalent to 1 billionth of a gram (10⁻⁹ g) or approximately 150,000-300,000 human diploid genome copies, depending on fragment size and quality. Context in NGS: Traditional NGS workflows often require 50-500 ng of high-quality DNA/RNA, but low-input methods (e.g., Twist’s cfDNA Library Prep Kit) can work with 1-10 ng or less. This is crucial for samples with limited material, such as: Circulating Cell-Free DNA (cfDNA): Found in blood (e.g., liquid biopsy for cancer MRD), yielding 5-50 ng from 2-4 mL plasma. FFPE Samples: Archived tumor tissues with degraded DNA/RNA, often yielding <10 ng. Single-Cell RNA-seq: Individual cells providing picogram amounts of RNA. Rare Disease or Prenatal Testing: Limited fetal DNA in maternal blood or biopsy samples.

Answer 40

Twist’s Advantage: The cfDNA Library Prep Kit’s ability to start with 1 ng (vs. competitors’ 10-20 ng minimum) is a game-changer for liquid biopsy, FFPE, or single-cell studies, reducing sample requirements and enabling research where material is scarce. Practical Implication: For researchers, this means they can sequence precious samples (e.g., pediatric tumors, rare disease biopsies) or perform repeated liquid biopsies without exhausting resources. Critical Consideration: Low input requires high-depth sequencing (e.g., 10,000x) to detect rare variants, which increases costs—highlight Twist’s cost-saving features (e.g., uniformity) to offset this.

Misc Deck (2) Flashcards

(69 cards)