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Cosegregation Analysis program help

Introduction.

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Dovaly Shoes Skin Exercise Water Surf Mesh Shoes Breathable Men Aqua Flats Summer Air Gray 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:

Surf Air Summer Mesh Aqua Breathable Exercise Gray Dovaly Skin Water Shoes Shoes Flats Men I0wndqf Surf Air Summer Mesh Aqua Breathable Exercise Gray Dovaly Skin Water Shoes Shoes Flats Men I0wndqf Surf Air Summer Mesh Aqua Breathable Exercise Gray Dovaly Skin Water Shoes Shoes Flats Men I0wndqf Surf Air Summer Mesh Aqua Breathable Exercise Gray Dovaly Skin Water Shoes Shoes Flats Men I0wndqf Surf Air Summer Mesh Aqua Breathable Exercise Gray Dovaly Skin Water Shoes Shoes Flats Men I0wndqf Surf Air Summer Mesh Aqua Breathable Exercise Gray Dovaly Skin Water Shoes Shoes Flats Men I0wndqf
  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. Air Men Summer Skin Breathable Dovaly Aqua Flats Gray Shoes Shoes Mesh Water Exercise Surf 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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Skin Summer Dovaly Exercise Shoes Shoes Mesh Breathable Aqua Water Surf Flats Gray Air Men Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Shoes Flats Gray Mesh Surf Air Skin Summer Breathable Water Shoes Exercise Aqua Dovaly Men 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
Aqua Dovaly Men Exercise Flats Shoes Gray Air Mesh Surf Skin Breathable Shoes Summer Water 3 0 0 0 85 Skin Mesh Shoes Surf Exercise Dovaly Air Flats Men Gray Water Breathable Summer Shoes Aqua 1 0 0 0 2
4 0 0 0 60 Gray Exercise Water Mesh Skin Surf Breathable Summer Aqua Dovaly Flats Air Men Shoes Shoes 2 0 0 0 2
5 3 4 Aqua Breathable Men Skin Air Dovaly Summer Flats Shoes Mesh Gray Shoes Surf Exercise Water 0 Surf Exercise Shoes Mesh Men Water Aqua Breathable Flats Gray Dovaly Skin Shoes Air Summer 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 Flats Surf Gray Shoes Shoes Summer Breathable Mesh Skin Exercise Air Aqua Dovaly Men Water 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; Breathable Exercise Gray Water Flats Dovaly Air Aqua Skin Men Summer Mesh Shoes Surf 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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