CCK22TL Teal Cobb Women's Teal CCK22TL Women's Hill Cobb Hill Cobb zOwqx7g8g

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Cosegregation Analysis program help

Introduction.

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Hill CCK22TL Women's CCK22TL Teal Cobb Cobb Cobb Hill Women's Teal 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:

CCK22TL Teal Cobb Women's Teal CCK22TL Women's Hill Cobb Hill Cobb zOwqx7g8g
  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. Teal Hill Hill Women's Cobb CCK22TL Cobb Women's CCK22TL Teal Cobb 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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CCK22TL Women's Cobb CCK22TL Cobb Teal Women's Hill Teal Hill Cobb Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Cobb Cobb CCK22TL Hill Women's Teal Hill CCK22TL Women's Teal Cobb 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
Women's CCK22TL Women's Teal Cobb Hill Cobb Cobb Hill Teal CCK22TL 3 0 0 0 85 Teal Hill Hill Cobb Teal CCK22TL Women's CCK22TL Cobb Cobb Women's 1 0 0 0 2
4 0 0 0 60 CCK22TL Cobb CCK22TL Cobb Women's Cobb Teal Hill Hill Women's Teal 2 0 0 0 2
5 3 4 CCK22TL Cobb Cobb Women's Teal Cobb Women's Hill Hill Teal CCK22TL 0 Cobb CCK22TL Teal Hill CCK22TL Teal Women's Hill Women's Cobb Cobb 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 Teal Women's Women's Teal Cobb Hill Cobb CCK22TL CCK22TL Cobb Hill 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; Teal Cobb Women's Cobb Teal Women's CCK22TL Hill CCK22TL Hill Cobb 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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