Prediction of lithium response using genomic data

• Published in: Scientific reports 2021-01, Vol.11 (1), p.1155-1155, Article 1155
• Main Authors: Stone, William, Nunes, Abraham, Akiyama, Kazufumi, Akula, Nirmala, Ardau, Raffaella, Aubry, Jean-Michel, Backlund, Lena, Bauer, Michael, Bellivier, Frank, Cervantes, Pablo, Chen, Hsi-Chung, Chillotti, Caterina, Cruceanu, Cristiana, Dayer, Alexandre, Degenhardt, Franziska, Del Zompo, Maria, Forstner, Andreas J., Frye, Mark, Fullerton, Janice M., Grigoroiu-Serbanescu, Maria, Grof, Paul, Hashimoto, Ryota, Hou, Liping, Jiménez, Esther, Kato, Tadafumi, Kelsoe, John, Kittel-Schneider, Sarah, Kuo, Po-Hsiu, Kusumi, Ichiro, Lavebratt, Catharina, Manchia, Mirko, Martinsson, Lina, Mattheisen, Manuel, McMahon, Francis J., Millischer, Vincent, Mitchell, Philip B., Nöthen, Markus M., O’Donovan, Claire, Ozaki, Norio, Pisanu, Claudia, Reif, Andreas, Rietschel, Marcella, Rouleau, Guy, Rybakowski, Janusz, Schalling, Martin, Schofield, Peter R., Schulze, Thomas G., Severino, Giovanni, Squassina, Alessio, Veeh, Julia, Vieta, Eduard, Trappenberg, Thomas, Alda, Martin
• Format: Article
• Language: English
• Subjects: 631/208; 692/308; Classification; Data collection; Datasets; Genomics; Humanities and Social Sciences; Learning algorithms; Lithium; Machine learning; Medicin och hälsovetenskap; multidisciplinary; Science; Science (multidisciplinary); Single-nucleotide polymorphism
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-80814-z

Predicting lithium response prior to treatment could both expedite therapy and avoid exposure to side effects. Since lithium responsiveness may be heritable, its predictability based on genomic data is of interest. We thus evaluate the degree to which lithium response can be predicted with a machine learning (ML) approach using genomic data. Using the largest existing genomic dataset in the lithium response literature (n = 2210 across 14 international sites; 29% responders), we evaluated the degree to which lithium response could be predicted based on 47,465 genotyped single nucleotide polymorphisms using a supervised ML approach. Under appropriate cross-validation procedures, lithium response could be predicted to above-chance levels in two constituent sites (Halifax, Cohen’s kappa 0.15, 95% confidence interval, CI [0.07, 0.24]; and Würzburg, kappa 0.2 [0.1, 0.3]). Variants with shared importance in these models showed over-representation of postsynaptic membrane related genes. Lithium response was not predictable in the pooled dataset (kappa 0.02 [− 0.01, 0.04]), although non-trivial performance was achieved within a restricted dataset including only those patients followed prospectively (kappa 0.09 [0.04, 0.14]). Genomic classification of lithium response remains a promising but difficult task. Classification performance could potentially be improved by further harmonization of data collection procedures.