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