{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Jay Shendure"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000265"],"host":["EGA"],"description":["EGA DAC EGAC00001000265"],"repository":["EGA"],"email":["shendure@uw.edu"],"pubmed_abstract":["<h4>Background</h4>Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availability of extended family members. While recent advances in single cell sequencing show promise, they remain limited by bias in DNA amplification and the rapid turnaround time (<36 h) required for fresh embryo transfer. Here, we describe and validate a method for inferring the inherited whole genome sequence of an embryo for preimplantation genetic diagnosis (PGD).<h4>Methods</h4>We combine haplotype-resolved, parental genome sequencing with rapid embryo genotyping to predict the whole genome sequence of a day-5 human embryo in a couple at risk of transmitting alpha-thalassemia.<h4>Results</h4>Inheritance was predicted at approximately 3 million paternally and/or maternally heterozygous sites with greater than 99% accuracy. Furthermore, we successfully phase and predict the transmission of an HBA1/HBA2 deletion from each parent.<h4>Conclusions</h4>Our results suggest that preimplantation whole genome prediction may facilitate the comprehensive diagnosis of diseases with a known genetic basis in embryos."],"pubmed_title":["Whole genome prediction for preimplantation genetic diagnosis."],"pubmed_authors":["Kumar Akash A, Ryan Allison A, Kitzman Jacob O JO, Wemmer Nina N, Snyder Matthew W MW, Sigurjonsson Styrmir S, Lee Choli C, Banjevic Milena M, Zarutskie Paul W PW, Lewis Alexandra P AP, Shendure Jay J, Rabinowitz Matthew M"],"pubmed_title_synonyms":["Diagnoses and Examination, Antemortem Diagnoses, screening, Postmortem Diagnoses, Antemortem Diagnosis, findings, familial, signs, whole genome, Diagnoses and Examinations, Diagnosis, Examination and Diagnoses, Diagnoses, genetic, Postmortem, Screenings, Mass Screenings, Examinations and Diagnoses, Mass, symptoms, Screening, inherited genetic, Antemortem, Diagnoses., Postmortem Diagnosis, constitutitional genetic, hereditary, Diagnose"],"pubmed_abstract_synonyms":["Networks, Scientific Bias, Antemortem Diagnosis, Prenatal Structures, Disorders, Inheritance, Kinship, PHGDHD, plant germ, Thalassemia-alpha, Diagnosis, Long Term, A10, Relative, Techniques, Single-Gene, SERA, A-THAL, diseases, Method, Epidemiologic Biase, symptoms, Life Cycle, diseases and disorders, Ecological, Transfer, Effect, alpha-Thalassemias, hereditary., Family Life Cycle, Ecological Biases, human disease, Kinship Network, Man (Taxonomy), Genomes, availability, Defects, NLS, A-thalassemia, 4930479N23, procedures, NLS1, Defect, Thalassemia alpha, hba2, genetic, CD31, Single-Gene Defect, Methodological Studies, Statistical Biases, Ecological Bias, Homo sapiens disease, Systematic, Family Life Cycles, Epidemiologic Biases, Long-Term Effects, Tubal Embryo Transfer, Diagnose, PGAD, Presumptive, screening, Hba, HBAM, Scientific, embryo, Genetic Disorders, Epidemiologic, Modern, HBH, familial, Longterm Effect, Ecological Fallacies, developing organism, Hba-a1, Procedure, alpha-Thalassemia, Hba-a2, Haplotype, results, PGDH, predicted, Diagnoses, Outcome Measurement Errors, Experimental, Postmortem, Screenings, Tubal Embryo Stage Transfer, Hba1, Examinations and Diagnoses, Relative Risks, Alpha thalassaemia, Diseases, Inborn Genetic Disease, Genetic Disorder, Truncation Bias, Postmortem Diagnosis, Filiation, Inborn, Diagnoses and Examination, Postmortem Diagnoses, Bias, Risk, SPCPJ732.04c, PDG, signs, Methodological, whole genome, Outcome Measurement, Hemoglobin H, Methodological Study, Prenatal Structure, A-Thalassemia, human, Experimental Bias, Life Cycles, Genetic Diseases, Outcome Measurement Error, disease, Thalassemia, Hereditary, inherited genetic, Alpha, Single-Gene Defects, other disease, human being, Family Member, Procedures, Effects, Ecological Fallacy, Truncation, Prenatal, Systematic Bias, Hereditary Diseases, Network, alpha-thalassemia trait, Human, Hbat1, method, Blastocyst Transfer, Alpha Thalassemia, Homo sapiens, Embryo Transfers, PGD, method used in an experiment, 6PGD, Mass, Studies, Screening, disease or disorder, Antemortem, Technique, Man, Fallacies, Genetic, Research, Longterm, Inborn Genetic, Aggregation, Diagnoses and Examinations, Long-Term, Structure, α-thalassemia, non-neoplastic, Study, embryonic organism, Disorder, Presumptive Structure, Embryonic Structure, disorder, Long-Term Effect, Kinship Networks, constitutitional genetic, Family, Single Gene Defects, Biase, HEL-S-113, Antemortem Diagnoses, Fallacy, Disease, Genetic Disease, findings, Family Research, disorders, Truncation Biases, medical condition, 3PGDH, Examination and Diagnoses, Family Members, Mass Screenings, Embryos, Long Term Effects, Errors, sequence, condition, 3-PGDH, background, techniques, alpha thalassemia, Relative Risk, Embryonic, Embryo, Risks, Biases, primary structure of sequence macromolecule, introduction, Longterm Effects, Presumptive Structures, plan specification, Hemoglobin H Disease, Hereditary Disease, developmental tissue, Error, Aggregation Bias, DEL, Families, Inborn Genetic Diseases, Modern Man, Statistical Bias, GRO:0005343, Statistical, Transfers, HBA-T3, HBA-T2, hereditary, Relatives, methodology"],"additional_accession":[]},"is_claimable":false,"name":"Data Committee for EMSEQ project","description":"Data Access Committee EGAC00001000265","dates":{"output":"2025-1-9"},"accession":"EGAC00001000265","cross_references":{"TAXONOMY":["9606"],"pubmed":["26019723"],"EGA":["EGAS00001001020","EGAD00001002257"]}}