| Acronym/Term | Definition | Notes |
|---|---|---|
| 10X | Another sequencing 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 | Similar to "flagging" | |
| bp | Base pair | |
| BQMS | Broad Quality Management System. Errors & variation tracking. | |
| BSP | Biological Samples Platform (obsolete) | |
| BTL | Broad Technology Labs | |
| Buffy coat | A particular layer of centrifuged blood/cell prep | |
| CAPA | Corrective Action Preventative Action - BQMS Issue Type | |
| CCLF | Cancer Cell Line Factory. Part of the Cancer group at Broad, GP LIMS/Analytics team working with them | |
| Cell line | ||
| cfDNA | Cell-free DNA | |
| CI | Continuous Improvement | |
| CLIA | Clinical Laboratory Improvement Amendments | https://www.aafp.org/practice-management/regulatory/clia.html |
| CMI | Count Me In. Cancer research project | |
CRSP | Clinical Research Sequencing Platform | |
| DCFM | Date Coverage First Met | |
| ExEx | Exome Express. Special system for faster results turnaround for some exome sequencing products. | |
| FFP / FFPE | Formaline fixed paraffin embedded (Tissue fixed in formaline and paraffin) | https://www.biochain.com/general/what-is-ffpe-tissue/ |
| GAP | Genomics Analysis Platform. Obsolete group/LIMS at Broad that has been absorbed into Genomics Platform | |
| GPLIM | Jira project for GP LIMS | |
| GSA | Global Screening Array. A chip type | |
| HS | Hybrid Selection or High Sensitivity | |
| IDT | A company that synthesizes DNA (e.g. for hybrid selection) | |
| Infinium | Genotyping platform for Illumina | |
| Insert size | Length of DNA fragments after shearing, before adapter ligation | |
| LC | Library Construction | |
| LCSET | Library construction set | |
| LIMS | Laboratory Information Management System | |
| Nexome | Exams processed with kits from Nextera? | |
| ORSP | Office of Research Subject Protection | |
| PCR | Polymerase chain reaction | |
| PDO | Product Order | |
| Pico | Pico-green, a fluorescent dye used to quant DNA | |
| Pond, bait, etc. | Hybrid selection terms, hyb sel is a process of creating exomes | |
| Pooling penalty | How similarly represented the different samples are in a pool of samples | |
| Qiagen | Company that makes extraction kits | |
| QTP | Quant Template Pool | |
| RGHQS | Regroup H Quality Scores | |
| RP | Research project | |
| SNP | Single nucleotide polymorphism | |
| SPRI | Solid Phase Reversible Immobiization (AMPure by Agencourt) | |
| SQM | ??? The group that does procurement and materials management | |
| SRS | Sample retrieval and storage | |
| TAG | The Analytics Group OR Translational Analysis Group | |
| TDE | Tableau Data Extract | |
| TOPMed | Trans-Omics for Precision Medicine | |
| TSCA | Process used for CCLF samples (among others) | |
| VBGP | Verily Broad Genomics Platform??? aka "Broad West" | |
| VVP | Volume verified pipetting. A liquid handler robot from Dynamic Devices | http://dynamicdevices.com/vvp-volume-verified-pipetting/ |
| WES (or WEX) | Whole Exome Sequencing | |
| WGS | Whole Genome Sequencing |
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