A framework for the detection of de novo mutations in family-based sequencing data

AbstractMotivationStructural Variation (SV) detection from short-read whole genome sequencing is error prone, presenting significant challenges for population or family-based studies of disease.ResultsHere we describe SV2, a machine-learning algorithm for genotyping deletions and duplications from paired-end sequencing data. SV2 can rapidly integrate variant calls from multiple structural variant discovery algorithms into a unified call set with high genotyping accuracy and capability to detect de novo mutations.Availability and ImplementationSV2 is freely available on GitHub (https://github.com/dantaki/SV2)

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Trio deep-sequencing does not reveal unexpected off-target and on-target mutations in Cas9-edited rhesus monkeys

Nature Communications ◽

10.1038/s41467-019-13481-y ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 8

Author(s):

Xin Luo ◽

Yaoxi He ◽

Chao Zhang ◽

Xiechao He ◽

Lanzhen Yan ◽

...

Keyword(s):

Rhesus Monkeys ◽

De Novo ◽

Preclinical Model ◽

Structural Variants ◽

Sequencing Data ◽

De Novo Mutations ◽

Target Region ◽

Long Read ◽

Target Effect

AbstractCRISPR-Cas9 is a widely-used genome editing tool, but its off-target effect and on-target complex mutations remain a concern, especially in view of future clinical applications. Non-human primates (NHPs) share close genetic and physiological similarities with humans, making them an ideal preclinical model for developing Cas9-based therapies. However, to our knowledge no comprehensive in vivo off-target and on-target assessment has been conducted in NHPs. Here, we perform whole genome trio sequencing of Cas9-treated rhesus monkeys. We only find a small number of de novo mutations that can be explained by expected spontaneous mutations, and no unexpected off-target mutations (OTMs) were detected. Furthermore, the long-read sequencing data does not detect large structural variants in the target region.

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HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data

BMC Genomics ◽

10.1186/s12864-018-4867-7 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 6

Author(s):

Xin Zhou ◽

Serafim Batzoglou ◽

Arend Sidow ◽

Lu Zhang

Keyword(s):

De Novo ◽

Sequencing Data ◽

De Novo Mutations

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Exonic Mosaic Mutations Contribute Risk for Autism Spectrum Disorder

10.1101/083428 ◽

2017 ◽

Cited By ~ 2

Author(s):

Deidre R. Krupp ◽

Rebecca A. Barnard ◽

Yannis Duffourd ◽

Sara A. Evans ◽

Ryan M. Mulqueen ◽

...

Keyword(s):

Autism Spectrum Disorder ◽

De Novo ◽

Large Family ◽

Recurrence Risk ◽

Autism Spectrum ◽

Spectrum Disorder ◽

Sequencing Data ◽

Full Cohort ◽

Risk Genes ◽

Family Based

AbstractGenetic risk factors for autism spectrum disorder (ASD) have yet to be fully elucidated. Postzygotic mosaic mutations (PMMs) have been implicated in several neurodevelopmental disorders and overgrowth syndromes. We systematically evaluated PMMs by leveraging whole-exome sequencing data on a large family-based ASD cohort, the Simons Simplex Collection. We found evidence that 11% of published single nucleotide variant (SNV) de novo mutations are potentially PMMs. We then developed a robust SNV PMM calling approach that leverages complementary callers, logistic regression modeling, and additional heuristics. Using this approach, we recalled SNVs and found that 22% of de novo mutations likely occur as PMMs in children. Unexpectedly, we found a significant burden of synonymous PMMs in probands that are predicted to alter splicing. We found no evidence of missense PMM burden in the full cohort. However, we did observe increased signal for missense PMMs in families without germline mutations in probands, which strengthens in genes intolerant to mutations. We also determined that 7-11% of parental mosaics are transmitted to children. Parental mosaic mutations make up 6.8% of all mutations newly germline in children, which has important implications for recurrence risk. PMMs intersect previously implicated high confidence and other ASD candidate risk genes, further suggesting that this class of mutations contribute to ASD risk. We also identified PMMs in novel candidate risk genes involved with chromatin remodeling or neurodevelopment. We estimate that PMMs contribute risk to 4-8% of simplex ASD cases. Overall, these findings argue for future studies of PMMs in ASD and related-disorders.

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HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data

10.1101/220830 ◽

2017 ◽

Cited By ~ 1

Author(s):

Xin Zhou ◽

Serafim Batzoglou ◽

Arend Sidow ◽

Lu Zhang

Keyword(s):

False Positive ◽

De Novo ◽

False Positives ◽

Sequencing Data ◽

De Novo Mutations ◽

Congenital Diseases ◽

Genome Wide ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Haplotype Information

AbstractBackgroundDe novo mutations (DNMs) are associated with neurodevelopmental and congenital diseases, and their detection can contribute to understanding disease pathogenicity. However, accurate detection is challenging because of their small number relative to the genome-wide false positives in next generation sequencing (NGS) data. Software such as DeNovoGear and TrioDeNovo have been developed to detect DNMs, but at good sensitivity they still produce many false positive calls.ResultsTo address this challenge, we develop HAPDeNovo, a program that leverages phasing information from linked read sequencing, to remove false positive DNMs from candidate lists generated by DNM-detection tools. Short reads from each phasing block are allocated to each of the two haplotypes followed by generating a haploid genotype for each putative DNM.HAPDeNovo removes variants that are called as heterozygous in one of the haplotypes because they are almost certainly false positives. Our experiments on 10X Chromium linked read sequencing trio data reveal that HAPDeNovo eliminates 80% to 99% of false positives regardless of how large the candidate DNM set is.ConclusionsHAPDeNovo leverages the haplotype information from linked read sequencing to remove spurious false positive DNMs effectively, and it increases accuracy of DNM detection dramatically without sacrificing sensitivity.

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Germline Missense Mutation of Deleted in Malignant Brain Tumor 1 (DMBT1) in Familial Mediastinal Neuroendocrine Cancer and in vitro Effects in Thyroid Cancer Cells

Neuroendocrinology ◽

10.1159/000504369 ◽

2019 ◽

Vol 110 (7-8) ◽

pp. 714-720

Author(s):

Ning Qu ◽

Rong-Liang Shi ◽

Tian Liao ◽

Sheng-Lin Huang ◽

Duo Wen ◽

...

Keyword(s):

Brain Tumor ◽

Missense Mutation ◽

Sanger Sequencing ◽

De Novo ◽

Susceptibility Gene ◽

Ectopic Expression ◽

Malignant Brain Tumor ◽

Sequencing Data ◽

De Novo Mutations

Background: Neuroendocrine tumors (NETs) rarely occur in the mediastinum and their etiology and pathogenesis are still unclear. Objectives: This study assessed inherited or de novo mutations in familial mediastinal NETs. Method: DNA samples from 4 patients were subjected to the whole-exome sequencing, and Sanger sequencing was used to identify Deleted in malignant brain tumor 1 (DMBT1) mutations in all 45 family members. Results: All patients showed a germline DMBT1 mutation at 4971C. Sanger sequencing data showed that 4 NETs and 2 carriers in the first patient’s family and 2 NETs and 4 carriers in the second patient’s family, respectively, had this DMBT1 mutation. The in vitro data showed that the ectopic expression of DMBT1 reduced tumor cell viability and migration by arresting the G1/S phase of the cell cycle. Conclusions: We identified a germline missense mutation in DMBT1D1657E as a susceptibility gene for familial mediastinal NETs.

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Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation

eLife ◽

10.7554/elife.46922 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 20

Author(s):

Thomas A Sasani ◽

Brent S Pedersen ◽

Ziyue Gao ◽

Lisa Baird ◽

Molly Przeworski ◽

...

Keyword(s):

Germline Mutation ◽

De Novo ◽

Primordial Germ Cell ◽

Mutation Accumulation ◽

Sequencing Data ◽

De Novo Mutations ◽

Cell Specification ◽

Mutational Spectra ◽

Germ Cell Specification ◽

Human Gametes

The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across families? Using sequencing data from 33 large, three-generation CEPH families, we observed significant variability in parental age effects on DNM counts across families, ranging from 0.19 to 3.24 DNMs per year. Additionally, we found that ~3% of DNMs originated following primordial germ cell specification in a parent, and differed from non-mosaic germline DNMs in their mutational spectra. We also discovered that nearly 10% of candidate DNMs in the second generation were post-zygotic, and present in both somatic and germ cells; these gonosomal mutations occurred at equivalent frequencies on both parental haplotypes. Our results demonstrate that rates of germline mutation accumulation vary among families with similar ancestry, and confirm that post-zygotic mosaicism is a substantial source of human DNM.

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Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder

Nature Communications ◽

10.1038/s41467-021-23453-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Masaki Nishioka ◽

An-a Kazuno ◽

Takumi Nakamura ◽

Naomi Sakai ◽

Takashi Hayama ◽

...

Keyword(s):

Bipolar Disorder ◽

Developmental Disorder ◽

De Novo ◽

Deleterious Mutations ◽

Loss Of Function ◽

Sequencing Data ◽

De Novo Mutations ◽

Significant Enrichment ◽

Postzygotic Mutations ◽

Depressive Episodes

AbstractBipolar disorder is a severe mental illness characterized by recurrent manic and depressive episodes. To better understand its genetic architecture, we analyze ultra-rare de novo mutations in 354 trios with bipolar disorder. For germline de novo mutations, we find significant enrichment of loss-of-function mutations in constrained genes (corrected-P = 0.0410) and deleterious mutations in presynaptic active zone genes (FDR = 0.0415). An analysis integrating single-cell RNA-sequencing data identifies a subset of excitatory neurons preferentially expressing the genes hit by deleterious mutations, which are also characterized by high expression of developmental disorder genes. In the analysis of postzygotic mutations, we observe significant enrichment of deleterious ones in developmental disorder genes (P = 0.00135), including the SRCAP gene mutated in two unrelated probands. These data collectively indicate the contributions of both germline and postzygotic mutations to the risk of bipolar disorder, supporting the hypothesis that postzygotic mutations of developmental disorder genes may contribute to bipolar disorder.

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A variant in TAF1 is associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features

10.1101/014050 ◽

2015 ◽

Cited By ~ 1

Author(s):

Jason O'Rawe ◽

Yiyang Wu ◽

Alan Rope ◽

Laura T. Jimenez Barrón ◽

Jeffrey Swensen ◽

...

Keyword(s):

Intellectual Disability ◽

De Novo ◽

Critical Role ◽

False Negative ◽

Disease Models ◽

Sequencing Data ◽

De Novo Mutations ◽

Genetic Syndrome ◽

Severe Intellectual Disability ◽

The Family

We describe the discovery of a new genetic syndrome, RykDax syndrome, driven by a whole genome sequencing (WGS) study of one family from Utah with two affected male brothers, presenting with severe intellectual disability (ID), a characteristic intergluteal crease, and very distinctive facial features including a broad, upturned nose, sagging cheeks, downward sloping palpebral fissures, prominent periorbital ridges, deep-set eyes, relative hypertelorism, thin upper lip, a high-arched palate, prominent ears with thickened helices, and a pointed chin. This Caucasian family was recruited from Utah, USA. Illumina-based WGS was performed on 10 members of this family, with additional Complete Genomics-based WGS performed on the nuclear portion of the family (mother, father and the two affected males). Using WGS datasets from 10 members of this family, we can increase the reliability of the biological inferences with an integrative bioinformatic pipeline. In combination with insights from clinical evaluations and medical diagnostic analyses, these DNA sequencing data were used in the study of three plausible genetic disease models that might uncover genetic contribution to the syndrome. We found a 2 to 5-fold difference in the number of variants detected as being relevant for various disease models when using different sets of sequencing data and analysis pipelines. We derived greater accuracy when more pipelines were used in conjunction with data encompassing a larger portion of the family, with the number of putative de-novo mutations being reduced by 80%, due to false negative calls in the parents. The boys carry a maternally inherited missense variant in a X-chromosomal gene TAF1, which we consider as disease relevant. TAF1 is the largest subunit of the general transcription factor IID (TFIID) multi-protein complex, and our results implicate mutations in TAF1 as playing a critical role in the development of this new intellectual disability syndrome.

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