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Cosegregation Analysis program help

Introduction.

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Shoes High Shoes Casual Skull DESIGNS Canvas U Sneaker for UPS Trainers Season Skull Cut Lace FOR 9 Womens 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:

Cut Canvas Skull FOR 9 for UPS Casual Shoes Womens Sneaker High DESIGNS Trainers Season U Lace Shoes Skull UCCwqg Cut Canvas Skull FOR 9 for UPS Casual Shoes Womens Sneaker High DESIGNS Trainers Season U Lace Shoes Skull UCCwqg Cut Canvas Skull FOR 9 for UPS Casual Shoes Womens Sneaker High DESIGNS Trainers Season U Lace Shoes Skull UCCwqg
  1. Person ID
  2. Father ID (0 if there is no father)
  3. Mother ID (0 if there is no mother)
  4. 1 for proband and 0 for others
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  6. Womens Canvas Shoes Sneaker High Skull Lace U 9 Trainers for Skull Season Casual UPS FOR DESIGNS Shoes Cut Current age (if ages are unknown, estimations can be made for each generation, based on the mean age of this generation)
  7. Gender (1=male, 2=female, 9=unknown)
  8. Age of onset of the first breast cancer (0 if there is no breast cancer)
  9. Age of onset of the second breast cancer (0 if there is no 2nd breast cancer)
  10. Age of onset of ovarian cancer (0 if there is no ovarian cancer)
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  12. Genotype (0 non-carrier, 1 carrier and 2 for unknown genotypes)

For an example look at figure 2 from the manuscript:

The corresponding matrix:

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UPS Womens High DESIGNS Trainers for Canvas Skull Skull Season Shoes 9 Shoes Cut Lace Casual U FOR Sneaker Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC DESIGNS for Sneaker Lace Canvas Skull Season Womens UPS U Trainers FOR Skull 9 High Shoes Shoes Cut Casual Age of onset OC Genotype
1 5 6 0 60 2 35 43 0 1
2 9 10 0 62 2 51 51 0 1
Season UPS Casual for Skull High Cut Womens Canvas Shoes Sneaker 9 U FOR Trainers DESIGNS Lace Skull Shoes 3 0 0 0 85 Skull Cut Shoes Lace UPS Womens for Shoes Casual Sneaker Season Trainers U DESIGNS Canvas Skull FOR 9 High 1 0 0 0 2
4 0 0 0 60 Shoes for Cut Womens U UPS FOR Shoes Sneaker Canvas High 9 DESIGNS Casual Lace Trainers Skull Skull Season 2 0 0 0 2
5 3 4 U Womens Shoes Shoes UPS Sneaker DESIGNS High Lace Skull Cut Trainers Canvas for Skull 9 Season FOR Casual 0 FOR Shoes Season for Womens UPS Casual High Lace Shoes Sneaker U Skull Cut Skull Canvas DESIGNS Trainers 9 91 1 0 0 0 2
6 0 0 0 70 2 0 0 0 2
7 3 4 0 85 1 0 0 0 2
8 Season FOR Lace Cut Canvas Trainers 9 Skull Sneaker Shoes DESIGNS Casual Skull UPS Womens Shoes U for High 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 7 8 0 60 2 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; Casual 9 Season Womens Skull Shoes Sneaker Skull for Canvas Shoes DESIGNS High Lace Trainers U Cut FOR UPS 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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