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Cosegregation Analysis program help

Introduction.

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Flat Womens Shoes amp; PU 18 Solids Leopards Gold Ballet 8600 Ballerina Shoes 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:

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  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. Sports for Grey Aqua Shoes Water Quick Women Walking Shoes Men Swim Dry Socks COLOV Running Pool Barefoot Beach HwtSq7Unp
  6. Solids Womens Gold 18 Shoes Leopards PU Flat 8600 Shoes Ballerina amp; Ballet 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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Ballet 8600 Ballerina amp; Shoes PU Leopards Flat 18 Shoes Gold Solids Womens Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Ballet Gold Womens Shoes PU Solids Ballerina 8600 Leopards Flat amp; 18 Shoes 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
8600 Womens Flat 18 PU Shoes Solids Ballerina Gold Shoes Leopards Ballet amp; 3 0 0 0 85 Flat Solids PU Ballet 18 Shoes Ballerina Gold Shoes amp; Womens Leopards 8600 1 0 0 0 2
4 0 0 0 60 18 Flat Ballet Shoes amp; Gold 8600 PU Ballerina Solids Womens Leopards Shoes 2 0 0 0 2
5 3 4 18 Flat Ballet Gold Shoes Womens Solids Ballerina 8600 amp; Leopards Shoes PU 0 Ballerina Shoes Solids PU Flat amp; 18 Ballet Gold Womens 8600 Leopards Shoes 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 Leopards Gold amp; PU 8600 Womens Shoes Solids 18 Ballet Shoes Ballerina Flat 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; Ballet Ballerina amp; Flat Leopards Solids 18 Gold PU Womens 8600 Shoes 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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