Haplotype inference in general pedigrees using the cluster variation method

Artificial Intelligence Based Hierarchical Clustering of Patient Types and Intervention Categories in Adult Spinal Deformity Surgery: Towards a New Classification Scheme that Predicts Quality and Value

STUDY DESIGN

Retrospective review of prospectively-collected, multicenter adult spinal deformity (ASD) databases.

OBJECTIVE

To apply artificial intelligence (AI)-based hierarchical clustering as a step toward a classification scheme that optimizes overall quality, value, and safety for ASD surgery.

SUMMARY OF BACKGROUND DATA

Prior ASD classifications have focused on radiographic parameters associated with patient reported outcomes. Recent work suggests there are many other impactful preoperative data points. However, the ability to segregate patient patterns manually based on hundreds of data points is beyond practical application for surgeons. Unsupervised machine-based clustering of patient types alongside surgical options may simplify analysis of ASD patient types, procedures, and outcomes.

METHODS

Two prospective cohorts were queried for surgical ASD patients with baseline, 1-year, and 2-year SRS-22/Oswestry Disability Index/SF-36v2 data. Two dendrograms were fitted, one with surgical features and one with patient characteristics. Both were built with Ward distances and optimized with the gap method. For each possible n patient cluster by m surgery, normalized 2-year improvement and major complication rates were computed.

RESULTS

Five hundred-seventy patients were included. Three optimal patient types were identified: young with coronal plane deformity (YC, n = 195), older with prior spine surgeries (ORev, n = 157), and older without prior spine surgeries (OPrim, n = 218). Osteotomy type, instrumentation and interbody fusion were combined to define four surgical clusters. The intersection of patient-based and surgery-based clusters yielded 12 subgroups, with major complication rates ranging from 0% to 51.8% and 2-year normalized improvement ranging from -0.1% for SF36v2 MCS in cluster [1,3] to 100.2% for SRS self-image score in cluster [2,1].

CONCLUSION

Unsupervised hierarchical clustering can identify data patterns that may augment preoperative decision-making through construction of a 2-year risk-benefit grid. In addition to creating a novel AI-based ASD classification, pattern identification may facilitate treatment optimization by educating surgeons on which treatment patterns yield optimal improvement with lowest risk.

LEVEL OF EVIDENCE

4.

A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree

Background

When studying genetic diseases in which genetic variations are passed on to offspring, the ability to distinguish between paternal and maternal alleles is essential. Determining haplotypes from genotype data is called haplotype inference. Most existing computational algorithms for haplotype inference have been designed to use genotype data collected from individuals in the form of a pedigree. A haplotype is regarded as a hereditary unit and therefore input pedigrees are preferred that are free of mutational events and have a minimum number of genetic recombinational events. These ideas motivated the zero-recombinant haplotype configuration (ZRHC) problem, which strictly follows the Mendelian law of inheritance, namely that one haplotype of each child is inherited from the father and the other haplotype is inherited from the mother, both without any mutation. So far no linear-time algorithm for ZRHC has been proposed for general pedigrees, even though the number of mating loops in a human pedigree is usually very small and can be regarded as constant.

Results

Given a pedigree with n individuals, m marker loci, and k mating loops, we proposed an algorithm that can provide a general solution to the zero-recombinant haplotype configuration problem in O(kmn + k²m) time. In addition, this algorithm can be modified to detect inconsistencies within the genotype data without loss of efficiency. The proposed algorithm was subject to 12000 experiments to verify its performance using different (n, m) combinations. The value of k was uniformly distributed between zero and six throughout all experiments. The experimental results show a great linearity in terms of execution time in relation to input size when both n and m are larger than 100. For those experiments where n or m are less than 100, the proposed algorithm runs very fast, in thousandth to hundredth of a second, on a personal desktop computer.

Conclusions

We have developed the first deterministic linear-time algorithm for the zero-recombinant haplotype configuration problem. Our experimental results demonstrated the linearity of its execution time in relation to the input size. The proposed algorithm can be modified to detect inconsistency within the genotype data without loss of efficiency and is expected to be able to handle recombinant and missing data with further extension.

Estimating population haplotype frequencies from pooled DNA samples using PHASE algorithm

Recent studies show that the PHASE algorithm is a state-of-the-art method for population-based haplotyping from individually genotyped data. We present a modified version of PHASE for estimating population haplotype frequencies from pooled DNA data. The algorithm is compared with (i) a maximum likelihood estimation under the multinomial model and (ii) a deterministic greedy algorithm, on both simulated and real data sets (HapMap data). Our results suggest that the PHASE algorithm is a method of choice also on pooled DNA data. The main reason for improvement over the other approaches is assumed to be the same as with individually genotyped data: the biologically motivated model of PHASE takes into account correlated genealogical histories of the haplotypes by modelling mutations and recombinations. The important questions of efficiency of DNA pooling as well as influence of the pool size on the accuracy of the estimates are also considered. Our results are in line with the earlier findings in that the pool size should be relatively small, only 2-5 individuals in our examples, in order to provide reliable estimates of population haplotype frequencies.

Identity-by-descent estimation and mapping of qualitative traits in large, complex pedigrees

Computing identity-by-descent sharing between individuals connected through a large, complex pedigree is a computationally demanding task that often cannot be done using exact methods. What I present here is a rapid computational method for estimating, in large complex pedigrees, the probability that pairs of alleles are IBD given the single-point genotype data at that marker for all individuals. The method can be used on pedigrees of essentially arbitrary size and complexity without the need to divide the individuals into separate subpedigrees. I apply the method to do qualitative trait linkage mapping using the nonparametric sharing statistic S(pairs). The validity of the method is demonstrated via simulation studies on a 13-generation 3028-person pedigree with 700 genotyped individuals. An analysis of an asthma data set of individuals in this pedigree finds four loci with P-values <10(-3) that were not detected in prior analyses. The mapping method is fast and can complete analyses of approximately 150 affected individuals within this pedigree for thousands of markers in a matter of hours.