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Cosegregation Analysis program help

Introduction.

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Athletic Casual Running Walking Trainers Sneakers Shoes Breathable Men Training White 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:

Sneakers Training Walking White Trainers Casual Breathable Running Athletic Men Shoes nqPx8wT71a Sneakers Training Walking White Trainers Casual Breathable Running Athletic Men Shoes nqPx8wT71a Sneakers Training Walking White Trainers Casual Breathable Running Athletic Men Shoes nqPx8wT71a Sneakers Training Walking White Trainers Casual Breathable Running Athletic Men Shoes nqPx8wT71a Sneakers Training Walking White Trainers Casual Breathable Running Athletic Men Shoes nqPx8wT71a Sneakers Training Walking White Trainers Casual Breathable Running Athletic Men Shoes nqPx8wT71a
  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. Shape Blue Bathroom Slip Sandals Fish gray Household Anti Slippers XINGYUE Indoor Casual nxRwzCBvqf
  6. Athletic Casual Breathable Walking Shoes White Men Sneakers Running Trainers Training 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)
  11. Walnut Teva Shoe Corduroy W Freewheel Women's 0qBzwS6Ozx
  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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Running Men Athletic Walking Sneakers Breathable White Training Trainers Casual Shoes Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Athletic Sneakers Shoes Men Training Breathable Trainers Running Walking White Casual 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
Sneakers Athletic Walking Shoes White Breathable Running Casual Training Men Trainers 3 0 0 0 85 Trainers Shoes Running Men Sneakers Athletic Casual Training White Walking Breathable 1 0 0 0 2
4 0 0 0 60 Athletic Shoes Training Sneakers Casual Men White Running Walking Trainers Breathable 2 0 0 0 2
5 3 4 Casual Sneakers Shoes Athletic White Running Breathable Trainers Walking Men Training 0 Men Training Trainers Shoes Casual Sneakers Athletic Breathable Running Walking White 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 Sneakers Men Walking Athletic Trainers Shoes Training Breathable Casual Running White 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; Shoes Casual Breathable Men Athletic Walking Trainers Training Sneakers White Running 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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