Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis

• Published in: BMC bioinformatics Vol. 18; no. 1; pp. 401 - 10
• Main Authors: Ostmeyer, Jared, Christley, Scott, Rounds, William H., Toby, Inimary, Greenberg, Benjamin M., Monson, Nancy L., Cowell, Lindsay G.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 07.09.2017; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Amino Acid Sequence; Antibodies; Antibody; Area Under Curve; Autoimmune diseases; B-Lymphocytes - metabolism; Bioinformatics; Biomedical and Life Sciences; Case depth; CDR3; Cerebrospinal fluid; Classifiers; Coding; Codons; Complementarity; Complementarity Determining Regions - chemistry; Complementarity Determining Regions - metabolism; Complementarity-determining region 3; Computational biology; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Datasets; Diagnosis; Diagnostic systems; Feasibility studies; High-Throughput Nucleotide Sequencing; Humans; Immune repertoire; Learning algorithms; Life Sciences; Lymphocytes; Lymphocytes B; Machine learning; Microarrays; Models, Statistical; Molecular diagnostic techniques; Multiple sclerosis; Multiple Sclerosis, Relapsing-Remitting - classification; Multiple Sclerosis, Relapsing-Remitting - diagnosis; Multiple Sclerosis, Relapsing-Remitting - immunology; Nervous System Diseases - classification; Nervous System Diseases - diagnosis; Nervous System Diseases - immunology; Neurological diseases; Ovarian cancer; Patients; Receptors; Research Article; ROC Curve; Sequence analysis (applications); Statistical classifier; Statistical methods; Statistics; T cell receptors; Multiple sclerosis; Antibody; CDR3; Immune repertoire; Statistical classifier; Machine learning
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-017-1814-6

Background Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and prognosticate diseases with a driving immune component by identifying repertoire sequence patterns associated with clinical phenotypes. Indeed, recent studies support the feasibility of this, demonstrating an association between repertoire-level summary statistics (e.g., diversity) and patient outcomes for several diseases. In our own prior work, we have shown that six codons in VH4-containing genes in B cells from the cerebrospinal fluid of patients with relapsing remitting multiple sclerosis (RRMS) have higher replacement mutation frequencies than observed in healthy controls or patients with other neurological diseases. However, prior methods to date have been limited to focusing on repertoire-level summary statistics, ignoring the vast amounts of information in the millions of individual immune receptors comprising a repertoire. We have developed a novel method that addresses this limitation by using innovative approaches for accommodating the extraordinary sequence diversity of immune receptors and widely used machine learning approaches. We applied our method to RRMS, an autoimmune disease that is notoriously difficult to diagnose. Results We use the biochemical features encoded by the complementarity determining region 3 of each B cell receptor heavy chain in every patient repertoire as input to a detector function, which is fit to give the correct diagnosis for each patient using maximum likelihood optimization methods. The resulting statistical classifier assigns patients to one of two diagnosis categories, RRMS or other neurological disease, with 87% accuracy by leave-one-out cross-validation on training data ( N  = 23) and 72% accuracy on unused data from a separate study ( N  = 102). Conclusions Our method is the first to apply statistical learning to immune repertoires to aid disease diagnosis, learning repertoire-level labels from the set of individual immune repertoire sequences. This method produced a repertoire-based statistical classifier for diagnosing RRMS that provides a high degree of diagnostic capability, rivaling the accuracy of diagnosis by a clinical expert. Additionally, this method points to a diagnostic biochemical motif in the antibodies of RRMS patients, which may offer insight into the disease process.