[IMPORTANT UPDATE] 22Q2 Correction of misidentified cell lines

Issues and Bugs
1

Cell line misidentification and contamination is a persistent challenge in cancer research, especially for projects such as DepMap which use hundreds of cancer cell lines. The International Cell Line Authentication Committee (ICLAC) maintains an extensive list of misidentified cell lines (Register of Misidentified Cell Lines – ICLAC). We reviewed all of the ICLAC version 11 cell lines in DepMap to determine if the stock used by DepMap was misidentified. This review process included checking the source of our stock and comparing SNP fingerprinting of the cell line and expected contaminant.

As expected, all of the ICLAC misidentified cell lines without known authentic stocks were also misidentified in DepMap. To maintain consistency with the literature, for these cell lines we have decided to keep the cell line name but update the metadata to align with the contaminant. This means that if a lung cancer cell line is contaminated with a cervical cancer cell line we have updated the lineage to cervix. We have also added a parent DepMap ID for these cell lines to indicate that they are derivatives.

For most of the ICLAC misidentified cell lines where authentic stocks are available, DepMap has the correct stock. The one exception is NCIH1339 (ACH-000921). Using STR- and SNP-fingerprinting, we also identified three other cell line misidentifications that are specific to DepMap.

Misidentifications with authentic stock:

  • NCIH1339 (ACH-000921) is actually an NCIH157 or NCIH1264 derivative. This misidentification is documented by ICLAC and seems to affect a number of papers. We have confirmed that the DepMap NCIH1339 stock matches NCIH157 or NCIH1264 with STR fingerprinting. Since authentic stocks of NCIH1339 are available from the originator, we have decided to relabel our NCIH1339 omics, RNAi, CRISPR, and compound sensitivity data as NCIH157DM (ACH-000921) to indicate that it is from an NCIH157 or NCIH1264 derivative.

DepMap specific misidentifications:

  • HSB2 (ACH-001737) is actually a CTV1 (ACH-002222) derivative. SNP-fingerprinting revealed that our omics data for HSB2 and CTV1 are isogenic, but according to the literature these cell lines are not from the same patient. Based on characteristic mutations documented by Atak et. al. we have determined that our HSB2 stocks are actually from a CTV1 derivative. Since this cell line has a distinct copy number profile from CTV1, we have decided to relabel our HSB2 omics and CRISPR data as CTV1DM (ACH-001737) and annotate it as a CTV1 derivative.

  • COLO699 (ACH-001041) is actually a CHL1 (ACH-000931) derivative. SNP-fingerprinting revealed that our omics data for COLO699 and CHL1 is isogenic, but according to the literature these cell lines are not from the same patient. Given that our COLO699 expression data is similar to expression data from CHL1 and other skin lines, but COLO699 is a lung line, we have determined that our COLO699 stocks are actually from a CHL1 derivative. Since this cell line has a distinct copy number profile from CHL1, we have decided to relabel our COLO699 omics, CRISPR, and RNAi data as CHL1DM (ACH-001041) and annotate it as a CHL1 derivative.

  • HS571T (ACH-001092) is actually a TOV112D (ACH-000048) derivative. SNP-fingerprinting revealed that our omics data for HS571T and TOV112D are isogenic but according to the literature these cell lines are not from the same patient. Based on the fact that our HS571T data has the TP53 Arg175His mutation characteristic of TOV112D (Characterization of four novel epithelial ovarian cancer cell lines - PubMed), we have determined that our HS571T stocks are actually from a TOV112D derivative. Since we only have legacy hybrid capture and SNP array data for HS571T we have decided to remove this cell line from our data.

Misidentification with lineage change:

  • SLR20 (ACH-000127) is actually a T24 (ACH-000018) derivative. The lineage of SLR24 has been changed from kidney to urinary tract.

  • SF767 (ACH-000490) is actually a ME180 (ACH-001359) derivative. The lineage of SF767 has been changed from central nervous system to cervix.

  • BGC823 (ACH-001017) and GLC82 (ACH-001071) are actually HELA (ACH-001086) derivatives. The lineages of BGC823 (gastric) and GLC82 (lung) have been changed to cervix.

  • GRM (ACH-001072) is actually a PSN1 (ACH-000320) derivative. The lineage of GRM has been changed from skin to pancreas.

Misidentification without lineage change:

Some metadata values have been updated for the following cell lines, but since they are derivatives of a cell line with the same lineage, the lineage annotation has not changed. Additional information about these cell lines can be found in the depmap_public_comments column of the same_info file.

  • ONCODG1 (ACH-000013)

  • GOS3 (ACH-000027)

  • KPL1 (ACH-000028)

  • PLB985 (ACH-000034)

  • U118MG (ACH-000040)

  • SLR24 (ACH-000272)

  • MELHO (ACH-000450)

  • KMS21BM (ACH-000598)

  • LN443 (ACH-000673)

  • MDAMB435S (ACH-000884)

  • AZ521 (ACH-001015)

  • CGTHW1 (ACH-001023)

  • COLO775 (ACH-001043)

  • COLO818 (ACH-001044)

  • KCIMOH1 (ACH-001098)

  • KP1N (ACH-001107)

  • YMB1 (ACH-001249)

  • SW527 (ACH-001825)

  • GT3TKB (ACH-002122)

  • H513 (ACH-002138)

  • K5 (ACH-002148)

  • MKN28 (ACH-002161)

  • NCIH1304 (ACH-002169)

  • OVMIU (ACH-002183)

  • YMB1E (ACH-002208)

  • BE13 (ACH-002216)

  • ETK1 (ACH-002237)

  • SKMG1 (ACH-002304)

  • JHU028 (ACH-002337)

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