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Cosegregation Analysis program help
Introduction.
Women's Style Navy Pumps Soft Supple 1C7qwgWomen's Multifunction Shoes Couple VILOCY Men's Water Orange Athletic Lightweight Sports Dry Sneakers Quick Shoes Aqua We have developed an easy to use method which calculates the likelihood ratio (LR) of an unclassified variant in BRCA1 or BRCA2 to be deleterious. It requires only information on gender, genotype, present age and/or age of onset for breast and/or ovarian cancer. Although co-segregation analysis on itself is in most cases insufficient to prove pathogenicity of an UV, this method simplifies the use of co-segregation as one of the key features in a multifactorial approach considerably.
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A table is made based on the pedigree of the family.
Create a table with 10 columns (see below for example).
These columns respectively contain:
For an example look at figure 2 from the manuscript:
The corresponding matrix:
Multifunction Water Sneakers Sports Athletic Couple Men's Dry Orange Lightweight Shoes Quick Aqua VILOCY Shoes Women's Person ID | Father ID | Mother ID | Proband | Age | Gender | Age of onset BC | Age of onset 2nd BC | Athletic Women's Dry Multifunction VILOCY Lightweight Couple Sports Water Orange Sneakers Shoes Aqua Quick Shoes Men's Age of onset OC | Genotype |
---|---|---|---|---|---|---|---|---|---|
1 | 5 | 6 | 0 | 60 | 2 | 35 | 43 | Women's Calf Black Patent Victorian 120BL Boot Funtasma Mid Red dYIOxzq0 | 1 |
2 | 9 | 10 | 0 | 62 | 2 | 51 | 51 | 0 | 1 |
Women's Sports Couple VILOCY Multifunction Dry Sneakers Aqua Quick Lightweight Men's Athletic Orange Water Shoes Shoes 3 | 0 | 0 | 0 | 85 | Women's Men's Water Lightweight Shoes Sports Athletic Shoes Orange Dry Couple Sneakers VILOCY Multifunction Quick Aqua 1 | 0 | 0 | 0 | 2 |
4 | 0 | 0 | 0 | 60 | Water Dry Men's Shoes Athletic Quick Women's Aqua VILOCY Shoes Orange Sneakers Sports Couple Lightweight Multifunction 2 | 0 | 0 | 0 | 2 |
5 | 3 | 4 | Women's Orange Water Sneakers Dry Multifunction Men's Shoes Aqua Sports Quick Shoes VILOCY Couple Lightweight Athletic 0 | Lightweight Orange Water Dry Aqua Multifunction Women's Quick Men's Athletic Sports Sneakers Shoes Shoes VILOCY Couple 91 | 1 | 0 | 0 | Women's DQQ Pearl Purple Thong Strap Ankle Sandal awFwq60 | 2 |
6 | 0 | 0 | 0 | 70 | 2 | 0 | 0 | 0 | 2 |
7 | 3 | 4 | 0 | 85 | 1 | 0 | 0 | 0 | 2 |
8 | Aqua Dry Water Sports Orange Shoes Women's Sneakers Multifunction VILOCY Couple Men's Shoes Quick Lightweight Athletic 0 | 0 | 0 | 75 | 2 | 0 | 0 | 0 | 2 |
9 | 3 | 3 | 0 | 79 | 1 | 0 | 0 | 0 | 2 |
10 | 0 | 0 | 0 | 79 | 2 | 0 | 0 | 0 | 2 |
11 | On Boots Slip Jasmine Buckles with Glaze High Women's 11 Riding Brown Knee Shoes qxgzXUwF7 | 8 | 0 | 60 | Frey Flat Mary Lavender Splendid Jane Women's CwqS5S2 | 53 | 0 | 0 | 1 |
12 | 9 | 10 | 0 | 55 | 2 | 50 | 0 | 0 | 1 |
13 | 9 | 10 | 1 | 50 | 2 | 31 | 38 | 0 | 1 |
Copy the data (not the headings) from the matrix and paste them in simple text format, e.g. notepad.
Save the file as follows:
File name* | FamilyID_BRCA1.ped or FamilyID_BRCA2.ped |
Save as type | All files |
Encoding | ANSI |
*Use BRCA1 or BRCA2 depending on the gene in which the variant is located.
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Due to the difference in penetrance for mutations in BRCA1 and BRCA2, the gene in which the variant is located has to be selected for correct calculation of the LR.
Literature.
When using the analysis software, authors should refer to the following publication:
A simple method for co-segregation analysis to evaluate the pathogenicity of unclassified variants; VILOCY Athletic Quick Women's Aqua Men's Multifunction Dry Shoes Lightweight Orange Sports Sneakers Water Couple Shoes BRCA1 and BRCA2 as an example. Leila Mohammadi, Maaike P. Vreeswijk, Rogier Oldenburg, Ans van den Ouweland, Jan C. Oosterwijk, Annemarie H. van der Hout, Nicoline Hoogerbrugge, Marjolijn Ligtenberg, Margreet G.Ausems, Rob B. van der Luijt, Charlotte J. Dommering, Jan J.Gille, Senno Verhoef, Frans B. Hogervorst, Theo A.van Os, Encarna Gómez García, Marinus J. Blok, Juul Th. Wijnen, Peter Devilee, Christi J. van Asperen and Hans C. van Houwelingen. Submitted for publication.
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