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Cosegregation Analysis program help

Introduction.

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11 Justin Inch Men's Riding Bent Valance Boot Crazy Cowhide Rail Miel Boots 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
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  6. Justin Cowhide Crazy 11 Inch Bent Men's Boots Miel Boot Valance Riding Rail 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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Bent 11 Boot Men's Justin Inch Cowhide Boots Miel Riding Crazy Valance Rail Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Rail Boot Valance Riding Bent Men's Crazy Miel Cowhide Boots Justin 11 Inch 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
Riding Miel 11 Boot Valance Boots Cowhide Bent Inch Men's Crazy Justin Rail 3 0 0 0 85 Boots Men's Justin Valance Crazy Rail Bent Riding Inch Boot Miel Cowhide 11 1 0 0 0 2
4 0 0 0 60 Rail Justin Miel 11 Cowhide Boots Men's Riding Inch Crazy Bent Boot Valance 2 0 0 0 2
5 3 4 Cowhide Valance Justin Boots Miel Men's Crazy Rail Bent Boot Inch Riding 11 0 11 Boot Justin Cowhide Riding Valance Boots Rail Inch Men's Bent Crazy Miel 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 Miel Rail Cowhide Justin Riding Men's Valance Boot Bent Inch Boots Crazy 11 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; Bent Valance Men's Rail Riding 11 Justin Cowhide Boots Miel Crazy Inch Boot 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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