An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs

On the prevalence and role of epistasis in shaping fitness within and between populations

The role of epistasis – inter-dependent contributions of alleles to fitness – in shaping genetic variation within and between populations is an important question in evolutionary biology with significant implications for our understanding of the factors contributing to phenotypic variation. While epistasis has been shown to play an important role in evolutionary processes such as speciation and adaptive evolution, many aspects of this role remains poorly understood. In particular, there is much debate on whether observing prevalent epistasis in evolution can be taken as evidence for functional epistasis that is relevant to selectable variation. Here, we studied the nature of epistasis in protein evolution, and found a high prevalence of epistatic interactions between amino acid sites in the human genome. We showed that these interactions can help improve accuracy of predicting the impact of genetic variation on the protein structure and function. We also showed that hypothesis-driven search for epistasis in natural populations can detect genomic signatures of epistasis in humans.El papel de la epistasia - contribuciones interdependientes de alelos a la adecuación biológica - en la conformación de la variación genética dentro y entre poblaciones es una cuestión importante en la biología evolutiva con importantes implicaciones para nuestra comprensión de los factores que contribuyen a la variación fenotípica. Mientras la epistasia se ha demostrado que desempeña un papel importante en los procesos evolutivos como la especiación y evolución adaptativa, muchos aspectos de esta función siguen siendo poco conocidos. En particular, hay mucho debate sobre si la observación de epistasia frecuente en la evolución puede ser tomada como evidencia de epistasia funcional que es relevante a la variación heredable. Aquí, se estudió la naturaleza de la epistasia en la evolución de proteínas, y encontramos una alta prevalencia de interacciones epistaticas entre sitios de aminoácidos en el genoma humano. Hemos demostrado que estas interacciones pueden ayudar a mejorar la precisión de predecir el impacto de la variación genética en la estructura y función de las proteínas. También se puso de manifiesto que la búsqueda de investigación basada en hipótesis por epistasia en poblaciones naturales puede detectar firmas genómicas de epistasia en los humanos

On the prevalence and role of epistasis in shaping fitness within and between populations

The role of epistasis – inter-dependent contributions of alleles to fitness – in shaping genetic variation within and between populations is an important question in evolutionary biology with significant implications for our understanding of the factors contributing to phenotypic variation. While epistasis has been shown to play an important role in evolutionary processes such as speciation and adaptive evolution, many aspects of this role remains poorly understood. In particular, there is much debate on whether observing prevalent epistasis in evolution can be taken as evidence for functional epistasis that is relevant to selectable variation. Here, we studied the nature of epistasis in protein evolution, and found a high prevalence of epistatic interactions between amino acid sites in the human genome. We showed that these interactions can help improve accuracy of predicting the impact of genetic variation on the protein structure and function. We also showed that hypothesis-driven search for epistasis in natural populations can detect genomic signatures of epistasis in humans.El papel de la epistasia - contribuciones interdependientes de alelos a la adecuación biológica - en la conformación de la variación genética dentro y entre poblaciones es una cuestión importante en la biología evolutiva con importantes implicaciones para nuestra comprensión de los factores que contribuyen a la variación fenotípica. Mientras la epistasia se ha demostrado que desempeña un papel importante en los procesos evolutivos como la especiación y evolución adaptativa, muchos aspectos de esta función siguen siendo poco conocidos. En particular, hay mucho debate sobre si la observación de epistasia frecuente en la evolución puede ser tomada como evidencia de epistasia funcional que es relevante a la variación heredable. Aquí, se estudió la naturaleza de la epistasia en la evolución de proteínas, y encontramos una alta prevalencia de interacciones epistaticas entre sitios de aminoácidos en el genoma humano. Hemos demostrado que estas interacciones pueden ayudar a mejorar la precisión de predecir el impacto de la variación genética en la estructura y función de las proteínas. También se puso de manifiesto que la búsqueda de investigación basada en hipótesis por epistasia en poblaciones naturales puede detectar firmas genómicas de epistasia en los humanos

Estimating the rate of irreversibility in protein evolution

Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function.This work was supported by Plan Nacional grant BFU2009-09271 from the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado Universitario) program grant AP2008-01888 from the Spanish Ministry of Education to O.S

Estimating the rate of irreversibility in protein evolution

Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function.This work was supported by Plan Nacional grant BFU2009-09271 from the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado Universitario) program grant AP2008-01888 from the Spanish Ministry of Education to O.S

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system.Financial support was provided by EMBO and the DFG SFB 670 ‘Zellautonome Immunität’ to M.L., DFG SFB 680 ‘Molecular basis of evolutionary innovation’ to T.W., DFG SPP1819 to M.L. and T.W., the HHMI International Early Career Scientist Programme (55007424), MINECO (Sev-2012-0208), AGAUR programme (2014 SGR 0974), and an ERC Starting Grant (335980_EinME) to F.K., the European Molecular Biology Laboratory to J.M., the Wellcome Trust to K.H. (zebrafish genome sequencing project) and the National Human Genome Research Institute (NHGRI) grant HG002659 to G.K.L. (gene annotation), and a grant from the Volkswagen Foundation to P.H.S

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy

© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. The influence of genetic background on driver mutations is well established; however, the mechanisms by which the background interacts with Mendelian loci remain unclear. We performed a systematic secondary-variant burden analysis of two independent cohorts of patients with Bardet–Biedl syndrome (BBS) with known recessive biallelic pathogenic mutations in one of 17 BBS genes for each individual. We observed a significant enrichment of trans-acting rare nonsynonymous secondary variants in patients with BBS compared with either population controls or a cohort of individuals with a non-BBS diagnosis and recessive variants in the same gene set. Strikingly, we found a significant over-representation of secondary alleles in chaperonin-encoding genes—a finding corroborated by the observation of epistatic interactions involving this complex in vivo. These data indicate a complex genetic architecture for BBS that informs the biological properties of disease modules and presents a model for secondary-variant burden analysis in recessive disorders

An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs