| Acronym/Term | Definition | Notes |
|---|---|---|
- “export” means going from BSP to non-BSP system like Mercury, GAP, or Squid (“export” will become obsolete when we move to everything being in mercury)
- 10X: another sequencer company (https://www.10xgenomics.com/)
- adapter = allows hybridization to the flow cell, contains molecular barcode index (special sequence of synthesized DNA)
- AoU: All of Us (https://allofus.nih.gov/)
- Blacklisting:
- bp: base pair
- BQMS = broad quality management system (errors & variation tracking)
- Buffy Coat = a particular layer of centrifuged blood/cell prep
- CCLF: Cancer Cell Line Factory (part of the cancer group at Broad, I've been part of a GP LIMS/Analytics team working with them)
- Cell line:
- cfDNA: cell-free DNA
- CI: Continuous Improvement
- CMI = Count Me In (cancer research project)
- CRSP: Clinical Research Sequencing Platform
- ExEx: Exome Express (special system for faster results turnaround for some exome sequencing products)
- Flow cell:
- GAP: Genomic Analysis Platform (obsolete group/LIMS at Broad that has been absorbed into Genomics Platform)
- GPLIM: Jira project for GP LIMS
- IDT: a company that synthesizes DNA (e.g. for hybrid selection)
- Infinium:
- insert size = length of DNA fragments after shearing, before adapter ligation
- LCSET = library construction set
- Nexome = exams processed with kits from Nextera?
- ORSP: Office of Research Subject Protection
- PCR: Polymerase chain reaction
- PDO = Product Order
- Pico (pico green): intercalating dye that fluoresces when bound to double-stranded DNA (dsDNA)
- Pico: Pico-green, a fluorescing dye used to quant DNA ( "PicoGreen is a fluorescent probe that binds dsDNA and forms a highly luminescent complex when compared to the free dye in solution")
- pond, bait, etc = hybrid selection terms, hyb sel is a process of creating exomes
- pooling penalty = has to do with how similarly represented the different samples are in a pool of samples
- Qiagen = company that makes extraction kits
- RP=research project
- SPRI: Solid Phase Reversible Immobilization (AMPure by Agencourt). Is this still used?
- TOPMed: Trans-Omics for Precision Medicine
- topoffs are bringing the lowest-coverage samples in a pool up to coverage
- TSCA is a process used for CCLF samples (among others)
- VBGP: Verily Broad Genomics Platform??? aka "Broad west" (confidential situation in which we run some sequencers at Google's Verily office in San Francisco)
- VVP: A liquid handler robot from Dynamic Devices (http://dynamicdevices.com/vvp-volume-verified-pipetting/)
- WGS: Whole Genome Sequencing
/wiki/spaces/DSDEGP/pages/475332729