Inferring chromosome segregation error stage and crossover in trisomic disorders with application to Down syndrome

Abstract

Errors in chromosome segregation during gametogenesis, such as nondisjunction (NDJ) errors, have severe consequences in human reproduction, and a better understanding of their etiology is of fundamental interest in genetics. Mapping NDJ errors to meiotic/mitotic stages typically requires proband-parent comparison, limiting its applicability. Herein, we develop Mis-segregation Error Identification through Hidden Markov Models (MeiHMM), a method for inferring NDJ error stage and crossover events based on only genomic data of trisomic probands. Guided by triallelic genotype/haplotype configurations, MeiHMM discerns the allelic origin at each locus, which informs NDJ error during gamete formation, without identifying the parental origin of the trisomy. In 152 Down syndrome (DS) cases, MeiHMM achieved an accuracy of 96.1% in classifying NDJ errors, with a sensitivity of 91.6% in crossover identification, compared to proband-parents trio analysis. 17% of Meiosis II errors were misclassified as Meiosis I, mainly due to small proximal crossover events. Applying MeiHMM to 509 children with DS-associated childhood leukemia, we demonstrate that NDJ error is associated with the age of disease onset, somatic genomic abnormalities, and prognosis. Thus, MeiHMM is an effective method for trisomic NDJ error classification and crossover identification that can be applied broadly to study the etiology of congenital aneuploidy conditions.

Fig. 1. Overview of MeiHMM.

A The types of chr 21 nondisjunction (NDJ) and their patterns of haplotypes along chr 21. Here, trisomy 21 is assumed to be of maternal origin. B Summary of the workflow to categorize chr 21 heterozygous SNPs. C Type 1 informative SNPs occur predominantly in two-haplotype blocks and type 2 informative SNPs occur predominantly in three-haplotype blocks. D Diagram of the hidden states and the observations of MeiHMM. E Distribution of the allele frequencies (AF) of two-copy alleles of chr 21 SNPs in simulated SNPs by sampling two (and duplicate one allele to make three alleles) or three alleles from gnomAD and AFLA references. F Distribution of the O/E ratio of hypothetical haplotypes. In panels E and F, yellow and blue colors indicate simulated values by assuming there are two or three haplotypes, respectively. G The results of MeiHMM of an example case with Meiosis I error. Red dashed lines indicate thresholds used to define type 1 (allele frequency <0.003) and type 2 (O/E ratio <0.1) informative SNPs. SNP Single-nucleotide polymorphism, ref alelle reference alelle, alt alelle alternative alelle, gnomAD Genome Aggregation Database, AFLA Allele Frequency Aggregator, AF allele frequency, O/E ratio ratio of observed vs expected frequency. Source data are provided as a Source Data file.

Fig. 2. Comparison of MeiHMM with trio analysis.

A Comparison of MeiHMM with trio analysis. B MeiHMM identified 87 of the 95 crossovers at similar positions and crossovers very close to the centromere leads to incorrect classifications. C Comparison of the minimum block size of correctly and incorrectly classified cases. D Frequencies of MI, MII, and mitotic errors identified by MeiHMM in 764 DS cases. E, F Distribution of the crossovers on chr 21 in (E) MI and (F) MII errors. MI meiosis I, MII meiosis II, DS Down syndrome, WGS whole genome sequencing. Source data are provided as a Source Data file.

Fig. 3. Applying MeiHMM to DS-ALL.

A Type of chromosome 21 NDJ errors of DS-ALL patients in specific age groups and molecular subtypes. Associations were tested using Chi Squared test. Nominal p-values were reported without adjusting for multiple comparisons. B, C P-values (by Chi Squared test) of the frequency of two-haplotype blocks across chromosome 21 genomic positions in different (B) age groups and (C) molecular subtypes compared to non-ALL DS cases. For (B and C), dashed red line indicate Bonferroni corrected p-value of 0.05. Size of red circles indicate the odds ratio of two-haplotype state comparing DS-ALL and non-ALL DS cases, when adjusted p-value < 0.05. D, E Kaplan–Meier estimates of the probability of (D) event-free survival or (E) overall survival of DS-ALL patients with meiosis I, meiosis II, and mitotic errors. Differences in survival were tested by log-rank test. Source data are provided as a Source Data file.