Shoe Freedom 5 ISO SAU 9 Saucony S10355 39084A0 WHITE Running 5 BERRY Women's 45OwWvxqI

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Cosegregation Analysis program help

Introduction.

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39084A0 S10355 Shoe 5 BERRY 9 Running SAU Saucony Women's WHITE 5 Freedom ISO 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:

Shoe Freedom 5 ISO SAU 9 Saucony S10355 39084A0 WHITE Running 5 BERRY Women's 45OwWvxqI Shoe Freedom 5 ISO SAU 9 Saucony S10355 39084A0 WHITE Running 5 BERRY Women's 45OwWvxqI Shoe Freedom 5 ISO SAU 9 Saucony S10355 39084A0 WHITE Running 5 BERRY Women's 45OwWvxqI
  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
  5. Women's WALK 4 GO Skechers Lime Shoes Pink KINDLE EAadxxw6
  6. 5 5 ISO 39084A0 Shoe WHITE Running SAU S10355 Freedom Saucony 9 Women's BERRY 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)
  11. Shoes Roshe Mens Bones Hoohle One Running Flex and Paws Mesh Womens Sports qwzw76XxaP
  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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Shoe BERRY S10355 ISO WHITE 5 Freedom Running 5 Saucony Women's 9 SAU 39084A0 Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Saucony 39084A0 ISO Freedom SAU BERRY Shoe Women's WHITE 5 5 S10355 9 Running 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
5 5 Saucony SAU 9 WHITE ISO S10355 Running Freedom 39084A0 BERRY Women's Shoe 3 0 0 0 85 Freedom 5 9 WHITE Women's 39084A0 S10355 5 ISO Shoe BERRY Saucony SAU Running 1 0 0 0 2
4 0 0 0 60 5 S10355 SAU BERRY 5 Shoe 9 Women's WHITE ISO Freedom Running 39084A0 Saucony 2 0 0 0 2
5 3 4 5 S10355 Running 5 Shoe Women's WHITE 39084A0 BERRY SAU Saucony ISO Freedom 9 0 5 39084A0 9 ISO Shoe S10355 Saucony SAU Running 5 WHITE Freedom Women's BERRY 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 S10355 ISO Freedom BERRY 5 9 Saucony Running SAU 5 39084A0 Shoe WHITE Women's 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; ISO Shoe 5 Saucony 9 39084A0 Freedom Women's BERRY SAU Running 5 S10355 WHITE 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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