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1. Additional file 1 of Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds

Author

Li, Zicheng, Wang, Zuoheng, Chen, Zhiyuan, Voegeli, Heidi, Lichtman, Judith H., Smith, Peter, Liu, Ju, DeWan, Andrew T., and Hoh, Josephine

Abstract

Additional file 1: Fig S1. The number of the nonsense genetic signatures (GS) for each breed. The y-axis represents the number of nonsense variants in GS represented by dots. The x-axis corresponds to each of the 76 breeds in the alphabetical order. Fig S2. Histogram showing the breed sample size distribution. The histogram showed the sample size within each valid breed enrolled in the GS discovery process. The minimal breed sample size was capped at three as shown in the histogram. Fig S3. Phylogenetic tree showing the breed membership of samples in the collection. Each sample was colored based on its breed label. Samples from the same breed were marked with the same color. a) Tree A includes 451 pure-bred dogs from 97 breeds in the collection. b) Tree B includes 412 pure-bred dogs from 76 valid breeds after removing potential wrongfully labeled samples. Fig S4. Pairwise genetic signature sharing between all 76 breeds. The 76 by 76 grid plot indicates the genome-wide GS sharing for all breed-pairs. The upper triangular part shows the standardized GS sharing score (See Methods). All scores were scaled between 0 and 1 with the darkest grid representing the highest GS sharing between Shetland sheepdog and Collie. The lower triangular part shows the absolute number of GS discovered across the genome. Similarly, the darker grid color indicates larger number of GS shared between two breeds. Fig S5. General pipeline of the population-frequency based variant analyzing tool. The flowchart showing the general workflow of the population frequency. Fig S6. Performance benchmark of the variant analyzing tool. a) Line plot showing the real-world run-time of using this tool to discover GS, BSGS and breed-pair unique shared GS in the dataset of 412 samples, when different number of CPUs were provided. b) The relative per-CPU efficiency for each of the three analyses when different number of CPUs were provided.

Published
2023
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2. Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds.

Author

Li, Zicheng, Wang, Zuoheng, Chen, Zhiyuan, Voegeli, Heidi, Lichtman, Judith H., Smith, Peter, Liu, Ju, DeWan, Andrew T., and Hoh, Josephine

Subjects
DOG breeds, NUCLEOTIDE sequencing, MICROSATELLITE repeats, PATTERN recognition systems, GENOME-wide association studies, SINGLE nucleotide polymorphisms, PHENOTYPES
Abstract

Background: In light of previous studies that profiled breed-specific traits or used genome-wide association studies to refine loci associated with characteristic morphological features in dogs, the field has gained tremendous genetic insights for known dog traits observed among breeds. Here we aim to address the question from a reserve perspective: whether there are breed-specific genotypes that may underlie currently unknown phenotypes. This study provides a complete set of breed-specific genetic signatures (BSGS). Several novel BSGS with significant protein-altering effects were highlighted and validated. Results: Using the next generation whole-genome sequencing technology coupled with unsupervised machine learning for pattern recognitions, we constructed and analyzed a high-resolution sequence map for 76 breeds of 412 dogs. Genomic structures including novel single nucleotide polymorphisms (SNPs), SNP clusters, insertions, deletions (INDELs) and short tandem repeats (STRs) were uncovered mutually exclusively among breeds. We also partially validated some novel nonsense variants by Sanger sequencing with additional dogs. Four novel nonsense BSGS were found in the Bernese Mountain Dog, Samoyed, Bull Terrier, and Basset Hound, respectively. Four INDELs resulting in either frame-shift or codon disruptions were found in the Norwich Terrier, Airedale Terrier, Chow Chow and Bernese Mountain Dog, respectively. A total of 15 genomic regions containing three types of BSGS (SNP-clusters, INDELs and STRs) were identified in the Akita, Alaskan Malamute, Chow Chow, Field Spaniel, Keeshond, Shetland Sheepdog and Sussex Spaniel, in which Keeshond and Sussex Spaniel each carried one amino-acid changing BSGS in such regions. Conclusion: Given the strong relationship between human and dog breed-specific traits, this study might be of considerable interest to researchers and all. Novel genetic signatures that can differentiate dog breeds were uncovered. Several functional genetic signatures might indicate potentially breed-specific unknown phenotypic traits or disease predispositions. These results open the door for further investigations. Importantly, the computational tools we developed can be applied to any dog breeds as well as other species. This study will stimulate new thinking, as the results of breed-specific genetic signatures may offer an overarching relevance of the animal models to human health and disease. [ABSTRACT FROM AUTHOR]

Published
2023
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