A Haplotyping Algorithm for Non-recombinant Pedigree Data Containing Missing Members

2007 ◽  
Author(s):  
Doan Dai Duong ◽  
Patricia A. Evans
Keyword(s):  
Pedigree Data

Pedigree Data Analysis With Crossover Interference

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1561-1566
Author(s):  
Sharon Browning
Keyword(s):  
Data Analysis ◽  
Linkage Analysis ◽  
Importance Sampling ◽  
Genetic Data ◽  
Genotype Data ◽  
Pedigree Data ◽  
Chi Square ◽  
Crossover Interference ◽  
Map Construction ◽  
Interference Models

AbstractWe propose a new method for calculating probabilities for pedigree genetic data that incorporates crossover interference using the chi-square models. Applications include relationship inference, genetic map construction, and linkage analysis. The method is based on importance sampling of unobserved inheritance patterns conditional on the observed genotype data and takes advantage of fast algorithms for no-interference models while using reweighting to allow for interference. We show that the method is effective for arbitrarily many markers with small pedigrees.

scholarly journals Evaluating Wild Germplasm Introgression into Autotetraploid Blueberry

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 614
Author(s):  
Diego Cabezas ◽  
Ivone de Bem Oliveira ◽  
Mia Acker ◽  
Paul Lyrene ◽  
Patricio R. Munoz
Keyword(s):  
Fruit Quality ◽  
Crop Improvement ◽  
Southeastern United States ◽  
Sandy Soils ◽  
Raw Material ◽  
Soluble Solids ◽  
Germplasm Resources ◽  
Wild Germplasm ◽  
Pedigree Data ◽  
Vaccinium Elliottii

Wild germplasm can be classified as the raw material essential for crop improvement. Introgression of wild germplasm is normally used in breeding to increase crop quality or resilience to evolving biotic and abiotic threats. Here, we explore the potential of introgressing Vaccinium elliottii into commercial blueberry germplasm. Vaccinium elliottii is a wild diploid blueberry species endemic to the southeastern United States that possesses highly desirable and economically important traits for blueberry breeding such as: short bloom to ripe period, adaptation to upland sandy soils, disease resistance, firmness, and pleasant flavor. To examine the potential of hybridization, we evaluated populations of interspecific hybrids across multiple stages of breeding (i.e., F1, F2, and backcrosses) in two crop seasons. We used our extensive pedigree data to generate breeding values for pre-breeding blueberry hybrid populations. Hybrid performance was evaluated considering fitness (i.e., plant vigor and plant height) in addition to evaluating six fruit-quality and marketable-related traits (i.e., size, firmness, acidity, soluble solids, weight, and yield). Overall, F2 and backcrosses rapidly achieved market thresholds, presenting values not significantly different from commercial blueberry germplasm. Our results confirmed the potential of exploiting the high genetic variability contained in V. elliottii for interspecific hybridization. Additionally, we developed germplasm resources that can be further evaluated and utilized in the breeding process, advancing selections for fruit quality and environmental adaptation.

scholarly journals The patterns of family genetic risk scores for eleven major psychiatric and substance use disorders in a Swedish national sample

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kenneth S. Kendler ◽  
Henrik Ohlsson ◽  
Jan Sundquist ◽  
Kristina Sundquist
Keyword(s):  
Genetic Risk ◽  
Molecular Genetic ◽  
National Sample ◽  
Autism Spectrum ◽  
Risk Scores ◽  
Pedigree Data ◽  
Obsessive Compulsive ◽  
Swedish Population ◽  
Compulsive Disorder ◽  
Genetic Risk Scores

AbstractTo clarify the structure of genetic risks for 11 major psychiatric disorders, we calculated, from morbidity risks for disorders in 1st–5th degree relatives controlling for cohabitation effects, in the Swedish population born between 1932 and 1995 (n = 5,830,014), the family genetic risk scores (FGRS) for major depression (MD), anxiety disorders (AD), obsessive-compulsive disorder (OCD), bipolar disorder (BD), schizophrenia (SZ), bulimia (BUL), anorexia nervosa (AN), alcohol use disorder (AUD), drug use disorder (DUD), ADHD, and autism-spectrum disorder (ASD). For all affected individuals, we calculated their mean standardized FGRS for each disorder. The patterns of FGRS were quite similar for MD and AD, and for AUD and DUD, but substantially less similar for BUL and AN, BD and SZ, and ADHD and ASD. While OCD had high levels of FGRS for MD and AD, the overall FGRS profile differed considerably from MD and AD. ADHD FGRS scores were substantially elevated in AUD and DUD. FGRS scores for BD, OCD, AN, ASD, ADHD, and especially SZ were relatively disorder-specific while genetic risk for MD and AD had more generalized effects. The levels of FGRS for BMI, coronary artery disease, and educational attainment across our disorders replicated prior associations found using molecular genetic methods. All diagnostic categories examined had elevated FGRS for many disorders producing, for each condition, an informative FGRS profile. Using a novel method which approximates, from pedigree data, aggregate genetic risk, we have replicated and extended prior insights into the structure of genetic risk factors for key psychiatric illnesses.

Familial Spontaneous Pneumothorax

PEDIATRICS ◽  
1979 ◽  
Vol 64 (2) ◽  
pp. 172-175
Author(s):  
William G. Wilson ◽  
Arthur S. Aylsworth
Keyword(s):  
Statistical Analysis ◽  
Spontaneous Pneumothorax ◽  
Autosomal Dominant ◽  
Autosomal Dominant Inheritance ◽  
Familial Occurrence ◽  
Review Of The Literature ◽  
Dominant Inheritance ◽  
Pedigree Data ◽  
Fathers And Sons ◽  
Male To Female

A family is described in which four persons in three generations suffered spontaneous pneumothoraces: a newborn, an infant, an adolescent, and an adult. Review of the literature reveals 61 reports of familial spontaneous pneumothorax in 22 families. The ratio of male to female cases is approximately 1.8. Affected parents and affected children (including affected fathers and sons) are seen in ten families, while affected siblings with unaffected parents are noted in 13 families. Consanguinity has not been reported. Although autosomal dominant inheritance has been suggested as an explanation of familial spontaneous pneumothorax, available pedigree data are not adequate for statistical analysis. Physicians should be aware of the familial occurrence of spontaneous pneumothorax so that members of such families may be appropriately managed when problems arise.

The protean phenotype of MSH6 pathogenic variants (PV) in Lynch syndrome (LS) patients (pts).

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 10537-10537
Author(s):  
Michelle J McSweeny ◽  
Susan Montgomery ◽  
Kristen Danielle Whitaker ◽  
Mary Beryl Daly ◽  
Michael J. Hall
Keyword(s):  
Skin Disease ◽  
Early Onset ◽  
Skin Lesions ◽  
Published Data ◽  
Pedigree Data ◽  
Skin Manifestations ◽  
Pathogenic Variants ◽  
Ca 50 ◽  
Uncertain Variant ◽  
Histologic Types

10537 Background: LS is among the most common hereditary cancer (CA) syndromes. PVs in MSH6 are 2-4 fold more common in the population (1/758) than those in MLH1 (1/1946) or MSH2 (1/2841), and are increasingly regarded as lower penetrance for CRC due to published data supporting later mean age of CRC onset and lower CRC risk. Unlike for MLH1/MSH2, NCCN 2020 CA risk estimates recognize only endometrial CA (EC) and CRC risks in MSH6+ carriers as clearly above SEER population estimates. Further, risks of other LS manifestations such as skin disease/Muir-Torre, ovarian CA (OC), and possible rare tumors in LS like sarcoma, have been minimally characterized in MSH6+ carriers. Methods: Pedigree data for 44 MSH6+ index (first-evaluated family member by our program) pts consecutively ascertained since 2009 at Fox Chase (FCCC) were reviewed. 1 pt w/a rare MSH6 uncertain variant w/personal history (PHx) of MSH6-expression deficient EC (age 50) and MSH6-deficient sebaceous skin CA (age 50) and a strong family history (FHx) c/w LS is also included here. 34% (15/44) index pts were referred to FCCC for cascade testing due to a known MSH6 PV in the family. Of the remaining 29 index pts, ascertainment included: 14% w/positive universal LS tumor screening, 21% w/early-onset or synchronous LS CA, 14% w/multi-gene panel for PHx of OC, 10% w/incidental MSH6+ result (2 had testing for PHx breast CA, 1 tumor genomic profiling), and 28% w/PHx and/or FHx of LS CA warranting genetic testing. Age of CA onset and path data were verified in > 90% index pts. Results: Index pts had a mean age of 55.5 yrs, and 77% were female. Overall, 11% (5/44) of MSH6+ index pts were found to have LS at diagnosis of synchronous primary CAs (3 EC/OC, 1 CRC/CRC, 1 CRC/EC), and 4/5 of these occurred <50 yrs. An additional 20% (9/44) index pts reported PHx of >2 metachronous LS CAs. OC was the presenting CA in 14% (6/44) female index pts; 2 additional index pts had rarer OC variants (Mullerian duct @ 41, primary peritoneal CA @ 50). Skin manifestations of LS were documented in 9.1% (4/44) index pts (3 sebaceous, 1 SCC in-situ/Bowen’s disease); 1 other family had documented sebaceous CAs in an FDR (father) but the 2 daughters seen @FCCC (both 30s) had yet to develop skin lesions. 2 index pts were found to have LS after developing early-onset breast CA (age 39) and contralateral breast CA (ages 50 and 54). Finally, 7% (3/44) index pts had a PHx of sarcoma: 2 were liposarcomas (ages 57 and 67), and 1 was a dermatofibrosarcoma. 2 other index pts had siblings w/childhood sarcomas. Conclusions: Our data, encompassing 44 MSH6+ pts evaluated in our clinic and consecutively ascertained, suggest MSH6 PV carriers develop synchronous primaries (11%), common and rare OC histologic types (18%), sarcomas (7%) and skin disease/Muir-Torre (9%). While common in the population and lower penetrance for CRC, MSH6 PV can behave in uncommon ways and may have significant extra-colonic CA risks such as OC, sarcoma and skin manifestations.

Extension of variance components approach to incorporate temporal trends and longitudinal pedigree data analysis

2002 ◽  
Vol 22 (3) ◽  
pp. 221-232 ◽  
Author(s):  
Mariza de Andrade ◽  
René Guéguen ◽  
Sophie Visvikis ◽  
Catherine Sass ◽  
Gérard Siest ◽  
...  
Keyword(s):  
Data Analysis ◽  
Variance Components ◽  
Temporal Trends ◽  
Pedigree Data
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