2023 ACMG Annual Clinical Genetics Meeting Digital Edition: Poster Gallery-The accuracy of variant-specific literature search results using LitVar2.

Pdf Summary

The study aimed to evaluate the accuracy and yield of variant-specific search results using LitVar2, a publicly-accessible search engine for genetic variant literature, compared to the manually-curated QCI tool. The researchers examined a subset of variants from the Horizon carrier screen panel and searched for literature specific to different coding effects, copy number variants, alternate/legacy names, co-occurring variants, and relevant articles not retrieved by QCI.<br /><br />The results showed that LitVar2 offered beneficial features such as highlighted keywords, search filters, retrieval of peer-reviewed publications, and monthly updates. However, it underperformed in retrieving literature for copy number variants and alternate/legacy names, as well as co-occurring variants.<br /><br />Out of the 42 variants searched for, QCI retrieved 371 papers compared to 158 papers retrieved by LitVar2. QCI also had a higher accuracy in finding papers with the variant of interest (VOI), with 99% of the papers containing the VOI compared to 67% retrieved by LitVar2.<br /><br />Of the 158 articles retrieved by LitVar2, 80 were additional articles not found in QCI. However, 65% of these articles did not contain the VOI. The remaining 35% contained the VOI not found in any other literature sources, but were not influential in determining the ACMG criteria for the variants.<br /><br />The study concluded that QCI retrieved more clinically relevant literature than LitVar2, suggesting that the two methods were not complementary. However, LitVar2 may still be a convenient platform for genetic labs curating literature, though not as the sole source of information.<br /><br />Overall, the study evaluated the accuracy of variant-specific literature search results using LitVar2 and compared it to the manual curation tool QCI. LitVar2 showed some limitations in retrieving certain types of variants, but still offered beneficial features for literature curation. QCI outperformed LitVar2 in terms of accuracy and number of relevant articles retrieved, suggesting that it may be a more reliable tool for variant curation.

Asset Subtitle

Presenting Author - Kim Gonzalez Hohlt, PhD; Co-Author - Sai Shruthi Chistavajjula, MS; Co-Author - Chiao L. Lo, PhD; Co-Author - Sara Pugsley, MS, CGC; Co-Author - Matthew Prego, MS; Co-Author - Trevor B. Smart, MS; Co-Author - Nina Sanapareddy, PhD; Submitter Only - J. Bryce Ortiz, PhD;

Meta Tag

Databases

Variant Detection

Co-Author Sai Shruthi Chistavajjula, MS

Co-Author Chiao L. Lo, PhD

Co-Author Sara Pugsley, MS, CGC

Co-Author Matthew Prego, MS

Co-Author Trevor B. Smart, MS

Co-Author Nina Sanapareddy, PhD

Presenting Author Kim Gonzalez Hohlt, PhD

Submitter Only J. Bryce Ortiz, PhD

Keywords

accuracy

yield

variant-specific search results

LitVar2

QCI tool

Horizon carrier screen panel

coding effects

copy number variants

alternate/legacy names

co-occurring variants