- WGS: Whole Genome Sequencing
- AoU: All of Us (https://allofus.nih.gov/)
- GAP: Genomic Analysis Platform (obsolete group/LIMS at Broad that has been absorbed into Genomics Platform)
- ExEx: Exome Express (special system for faster results turnaround for some exome sequencing products)
- CRSP: Clinical Research Sequencing Platform
- cfDNA: cell-free DNA
- IDT: a company that synthesizes DNA (e.g. for hybrid selection)
- VBGP: Verily Broad Genomics Platform??? aka "Broad west" (confidential situation in which we run some sequencers at Google's Verily office in San Francisco)
- 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)
- CI: Continuous Improvement
- VVP: A liquid handler robot from Dynamic Devices (http://dynamicdevices.com/vvp-volume-verified-pipetting/)
- 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")
- 10X: another sequencer company (https://www.10xgenomics.com/)
- SPRI: Solid Phase Reversible Immobilization (AMPure by Agencourt). Is this still used?
- bp: base pair
- PCR: Polymerase chain reaction
RP=research project
PDO = Product Order
LCSET = library construction set
BQMS = broad quality management system (errors & variation tracking)
pooling penalty = has to do with how similarly represented the different samples are in a pool of samples
CMI = Count Me In (cancer research project)
TSCA is a process used for CCLF samples (among others)
topoffs are bringing the lowest-coverage samples in a pool up to coverage
“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)
Qiagen = company that makes extraction kits
Pico (pico green): intercalating dye that fluoresces when bound to double-stranded DNA (dsDNA)
Buffy Coat = a particular layer of centrifuged blood/cell prep
Nexome = exams processed with kits from Nextera?
pond, bait, etc = hybrid selection terms, hyb sel is a process of creating exomes
insert size = length of DNA fragments after shearing, before adapter ligation
adapter = allows hybridization to the flow cell, contains molecular barcode index (special sequence of synthesized DNA)
/wiki/spaces/DSDEGP/pages/475332729