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Acronym/TermDefinitionNotes
10XAnother sequencing companyhttps://www.10xgenomics.com/
AdapterAllows hybridization to the flow cell, contains molecular barcode index (special sequence of synthesized DNA)
AoUAll of Ushttps://allofus.nih.gov/
BITSBroad Information Technology Services
BlacklistingSimilar to "flagging" 
bpBase pair
BQMSBroad Quality Management System. Errors & variation tracking.
BSPBiological Samples Platform (obsolete)
BTLBroad Technology Labs
Buffy coatA particular layer of centrifuged blood/cell prep
CAPACorrective Action Preventative Action - BQMS Issue Type
CCLFCancer Cell Line Factory. Part of the Cancer group at Broad, GP LIMS/Analytics team working with them
Cell line

cfDNACell-free DNA
CIContinuous Improvement
CLIAClinical Laboratory Improvement Amendmentshttps://www.aafp.org/practice-management/regulatory/clia.html
CMICount Me In. Cancer research project

CRSP

Clinical Research Sequencing Platform
DCFMDate Coverage First Met
ExExExome Express. Special system for faster results turnaround for some exome sequencing products.
FFP / FFPEFormaline fixed paraffin embedded (Tissue fixed in formaline and paraffin)https://www.biochain.com/general/what-is-ffpe-tissue/
GAPGenomics Analysis Platform. Obsolete group/LIMS at Broad that has been absorbed into Genomics Platform
GPLIMJira project for GP LIMS
GSAGlobal Screening Array. A chip type
HSHybrid Selection or High Sensitivity
IDTA company that synthesizes DNA (e.g. for hybrid selection)
InfiniumGenotyping platform for Illumina
Insert sizeLength of DNA fragments after shearing, before adapter ligation
LCLibrary Construction
LCSETLibrary construction set
LIMSLaboratory Information Management System
NexomeExams processed with kits from Nextera?
ORSPOffice of Research Subject Protection
PCRPolymerase chain reaction
PDOProduct Order
PicoPico-green, a fluorescent dye used to quant DNA
Pond, bait, etc.Hybrid selection terms, hyb sel is a process of creating exomes
Pooling penaltyHow similarly represented the different samples are in a pool of samples
QiagenCompany that makes extraction kits
QTPQuant Template Pool
RGHQSRegroup H Quality Scores
RPResearch project
SNPSingle nucleotide polymorphism
SPRISolid Phase Reversible Immobiization (AMPure by Agencourt)
SQM??? The group that does procurement and materials management
SRSSample retrieval and storage
TAGThe Analytics Group OR Translational Analysis Group
TDETableau Data Extract
TOPMedTrans-Omics for Precision Medicine
TSCAProcess used for CCLF samples (among others)
VBGPVerily Broad Genomics Platform??? aka "Broad West"
VVPVolume verified pipetting. A liquid handler robot from Dynamic Deviceshttp://dynamicdevices.com/vvp-volume-verified-pipetting/
WES (or WEX)Whole Exome Sequencing
WGSWhole Genome Sequencing



Additional resources

Broad Institute Acronyms (external link)

/wiki/spaces/DSDEGP/pages/475332729

/wiki/spaces/GAWB/pages/90341450

Broad/Illumina Genome Analyzer Boot Camp (to be viewed for reference about the Genomics Platform)

Picard Metrics Definitions

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