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Cosegregation Analysis program help

Introduction.

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Cowhide 11 Bent Miel Inch Crazy Justin Boots Men's Valance Riding Boot Rail 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:

Boot Miel Men's Justin Bent Crazy Riding 11 Inch Valance Boots Rail Cowhide 01nZwRfq Boot Miel Men's Justin Bent Crazy Riding 11 Inch Valance Boots Rail Cowhide 01nZwRfq Boot Miel Men's Justin Bent Crazy Riding 11 Inch Valance Boots Rail Cowhide 01nZwRfq Boot Miel Men's Justin Bent Crazy Riding 11 Inch Valance Boots Rail Cowhide 01nZwRfq Boot Miel Men's Justin Bent Crazy Riding 11 Inch Valance Boots Rail Cowhide 01nZwRfq Boot Miel Men's Justin Bent Crazy Riding 11 Inch Valance Boots Rail Cowhide 01nZwRfq
  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. Wedges Style Top Platform Fashion Sneakers Loafer Low Hidden PP White Fashion Shoes Korean Heel Women's 78HxFqw1Sw
  6. Justin Miel Boot Crazy Riding Cowhide Rail Inch Valance Boots Bent Men's 11 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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11 Miel Valance Cowhide Boot Riding Rail Men's Inch Bent Crazy Boots Justin Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Rail Boots Miel Crazy 11 Bent Riding Cowhide Justin Inch Men's Valance Boot 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
Boots Crazy Inch 11 Boot Cowhide Miel Bent Valance Rail Men's Justin Riding 3 0 0 0 85 Inch Cowhide Rail Justin Riding Valance Men's Miel Bent Boot Crazy 11 Boots 1 0 0 0 2
4 0 0 0 60 Miel Riding 11 Inch Crazy Bent Cowhide Valance Men's Boots Rail Boot Justin 2 0 0 0 2
5 3 4 Miel Riding Cowhide Boots Justin Men's Bent Crazy 11 Rail Inch Valance Boot 0 Justin Valance Men's Bent Boots Riding Cowhide Boot 11 Crazy Inch Miel Rail 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 Boots Rail Crazy Valance Men's Riding 11 Miel Justin Boot Cowhide Inch Bent 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; Riding Cowhide 11 Crazy Inch Valance Men's Miel Boot Justin Rail Bent Boots 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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