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I caught my father-in-law looking at gay porn and he sucked my cock, after which I cuckolded him. Racial bias can be an ugly thing. My family is Puerto Rican, and we moved to Davenport, Iowa when I was only three years old after my father had gotten a good job in a manufacturing plant there. The population in Davenport and the entire state is predominately white, so we stood out as being different. My name is Rolan, and I met Jennifer Jenthe girl who would later become my wife, half way through our junior year of high school when we were both sixteen years old.


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Try out PMC Labs and tell us what you think. Learn More. Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe a combined approach to identify and characterize a genetic disorder that leverages distantly related patients in a health system and population-scale mapping. We utilize genomic data to uncover components of distant pedigrees, in the absence of recorded pedigree information, in the multi-ethnic Bio Me biobank in New York City. By linking to medical records, we discover a locus associated with both elevated genetic relatedness and extreme short stature.

We link the gene, COL27A1with a little-known genetic disease, ly thought to be rare and recessive. Diseases often run in families. These disease are frequently linked to changes in DNA that are passed down through generations.

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Close family members may share these disease-causing mutations; so may distant relatives who inherited the same mutation from a common ancestor long ago. Geneticists use a method called linkage mapping to trace a disease found in multiple members of a family over generations to genetic changes in a shared ancestor.

This allows scientists to pinpoint the exact place in the genome the disease-causing mutation occurred. Using computer algorithms, scientists can apply the same technique to identify mutations that distant relatives inherited from a common ancestor. Belbin et al. In the experiments, the genomes of about 32, New Yorkers who have volunteered to participate in the BioMe Biobank and their health records were used to search for genetic changes linked to extremely short stature.

The search revealed that people who inherited two copies of this mutation from their parents were likely to be extremely short or to have bone and t problems. People who inherited one copy had an increased likelihood of t or bone problems. This mutation affects a gene responsible for making a form of protein called collagen that is important for bone growth.

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The analysis suggests the mutation first arose in a Native American ancestor living in Puerto Rico around the time that European colonization began. The mutation had ly been linked to a disorder called Steel syndrome that was thought to be rare.

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The experiments emphasize the importance of including diverse populations in genetic studies, as studies of people of predominantly European descent would likely have missed the link between this disease and mutation. During the past two decades major advances in deciphering the genetic basis of human disease have resulted in thousands of disorders that are now understood at a genetic level Hamosh et al. This progress has led to the integration of genomic sequencing in clinical care, especially for the diagnosis of rare genetic disease Bamshad et al. In the past few years, large national and international efforts Manolio et al.

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In parallel, many large regional and national biobank efforts Collins and Varmus, ; Ashley, ; Collins, are underway dating Davenport IA ricans enable the broad integration of genomics in health systems for genetic identification of disease Dewey et al. Such efforts have recently revealed clinically actionable variants Dewey et al. The increased promulgation of genomics in health systems represents an opportunity to improve diagnostic sensitivity for more precise therapeutic intervention and better health outcomes Ashley, Despite this progress, most genetic diseases are still under-diagnosed Abul-Husn et al.

A of barriers exist for wholesale genetic testing and diagnoses, including incomplete standardized guidelines for interpreting genetic evidence of disease Amendola et al. The latter is a particularly pernicious problem in non-European populations due to systematic biases in large genomic and clinical databases Popejoy and Fullerton, ; Petrovski and Goldstein, These challenges have led several research groups to attempt to genetically identify disease by examining patient health patterns using data from the Electronic Health Record EHR Gottesman et al.

EHRs have been used to clinically characterize well-known genetic disorders, but have been of limited success for the vast cadre of less-characterized or unknown disorders Blair et al. The gold standard of genetic disorder diagnosis involves testing both patient and family members to confirm Mendelian segregation of the suspected underlying pathogenic variant ClinGen et al. However, as genomic data becomes more ubiquitous in health systems, it can be used to detect genetic relationships in the absence of known family and pedigree dating Davenport IA ricans.

Specifically, components of pedigrees can be uncovered within the general population; particularly those that have experienced recent founder effects. Pairs of individuals who are related share genetic homology in the form of long genomic haplotypes.

These haplotypes are considered to be identical-by-descent IBD if they are inherited from a common ancestor without any intervening recombination. However, when IBD sharing does occur, the length of an IBD segment can remain long even between distantly related individuals. Detection of IBD haplotypes can allow for the identification of distantly related patients with a genetic disorder driven by a locus inherited from a founding ancestor who brought the disease mutation into a population Houwen et al. This is the principle underlying population-scale disease mapping approaches that combine IBD sharing and statistical association to discover novel disease loci, so called IBD-mapping.

By detecting genetic relatedness, as inferred by IBD sharing, we hypothesized that we may be able to detect hereditary forms of disease in an EHR-linked biobank. Participants are largely from the local Upper East Side, Harlem and Bronx communities, and represent broad ancestral, ethnic, cultural, and socioeconomic diversity. We initially focused on adult height, which is easily measurable, stable over the adult life course, and one of the most abundantly recorded clinical parameters in EHRs.

Height is known to be highly heritable and polygenic Visscher et al. Although, many genetic syndromes are known to cause short stature, most of the time no definitive etiology underlying short stature is found in patients. Here we used loci associated with elevated genetic relatedness as measured by IBD to map a locus underlying extreme short stature in the Bio Me biobank, and linked it to a known, but little characterized, collagen disorder ly thought to be rare.

By interrogating a large global diversity panel, we demonstrated that this variant is actually common in Puerto Rican populations. Furthermore, we leveraged the EHR to show ificant musculoskeletal disease in both heterozygous and homozygous patients, indicating the disease is not simply a recessive disorder as had ly been thought.

Finally, we showed how this work can generate broad insights for sustainable adoption and large-scale dissemination of genomic medicine. We observed that individuals had primary parent-child, sibling or secondary avuncular, grandparental relationship with another participant in BioMe, and we removed these individuals from all downstream analysis.

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Next we devised a strategy to divide the diverse Bio Me biobank into population groups for downstream analysis. Based on both self-reporting and patterns of genetic diversity observed in Bio Me participants, we stratified individuals into four broad population groups. The minimum length of 3 cM was chosen based on reports of elevated type I error in call rates of smaller lengths Gusev et al.

It is known that population-level rates of distant relatedness are observed to be particularly elevated after population bottlenecks i.

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We summed the length of all IBD-tracts shared between a given pair of individuals if they shared more than one tract and examined the distribution of pairwise sharing at a population level. This is congruent with reports of founder effects in both AJ populations Need et al. The x and y axis each represent relatedness coefficients kwhich describe the fraction of the genome that a given pair of individuals share Identically-by-State IBS. The y-axis represents k2, which is the fraction of the genome where a pair of individuals share 2 alleles IBS.

Each grey dot represents a pairwise relationship between two Bio Me participants. Directly related pairs of individuals can be identified based on observed levels of IBS sharing which is expected to be high for directly related individuals.

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Directly related individuals were detected in both the AA and HL populations. Global reference panels from the 1KGP are also represented, here colored based on their continental region, with African samples in blue, European samples in red, East Asian samples in purple, South Asian samples in yellow, and samples from the Americas in green.

Associated data

Bio Me participants fall across the spectrum of global diversity. A Principal component analysis PCA of Bio Me AA individuals grey reveal that the majority of individuals fall on a cline between the European red and African blue reference panels, suggesting that they have varying proportions of African and European admixture. A small of AA individuals cluster near the South Asian reference panel yellowinvestigation of questionnaire information for these individuals revealed them to mostly have been born in Trinidad and Tobago.

We suspect that this may be the result of recent admixture between Ashkenazi and Non-Ashkenazi Jewish Europeans. To restrict analysis to individuals likely to be of Puerto Rican ancestry we included individuals who reported recent Puerto Rican ancestry i.

Next we tested the hypothesis that rare, recessive disease variants may have arisen to appreciable frequency in the Puerto Rican founder population. We focused on height, a stable and ubiquitous health measure.

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We noted that 56 Puerto Ricans met the clinical definition of short stature Cohen et al. Membership in a clique indicates the sharing of a recent common ancestor at that locus, from which the homologous IBD tract was tly inherited.

The site frequency spectrum of IBD-cliques Figure 2—figure supplement 3 demonstrates an expected exponential distribution of clique sizes of 3—77 haplotypesrepresenting a class of rare IBD haplotypic alleles allelic frequency 0. To test whether any cliques of IBD haplotypes were ificantly associated with height we performed genome-wide association of height as a continuous trait under a recessive model using PLINKv1.

We restricted analysis to out of cliques that contained at least 3 individuals who were homozygous for the shared haplotype. The clique contains 59 individuals, 56 of whom are heterozygous and 3 are homozygous for the associated IBD haplotype.

Analysis was restricted to IBD-cliques where at least three individuals were homozygous. Only one IBD-clique achieved Bonferroni ificance at 9q B Distribution of height among Puerto Rican individuals who carry either 0,1 or 2 copies of the IBD-haplotype reveals a large recessive effect.

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C The minimum shared boundary of the ificant IBD-haplotype between the three homozygous individuals represented by the dashed blue line. The top panel depicts known genes at the 9q32 locus. The black dashed line represents 2 s. Individuals who fall below this threshold meet the clinical criteria for short stature. Individuals with recent, shared ancestry can co-inherit long tracts of the genome identical-by-descent IBD from a recent common ancestor RCA.

Haplotypes shared IBD here are indicated in red. Because IBD segments are broken up by meiosis, the probability of IBD sharing between any two individuals decreases with increasing genealogical distance. However, while the probability of IBD sharing decreases rapidly, long segments of IBD can persist between individuals even after they have been separated by many generations of meiosis.