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Cosegregation Analysis program help

Introduction.

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Skin Dovaly Gray Surf Shoes Shoes Summer Aqua Exercise Mesh Breathable Water Air Men Flats 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
  5. Black Lugz Men's Boot Hi Brigade 1qAI1Hrgw
  6. Mesh Water Surf Summer Shoes Dovaly Air Men Exercise Breathable Flats Aqua Skin Shoes Gray 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:

SHOE 700712 BLACK 03N batini SPORTS BTN Black zwTqdd6nLakota Bootie Women's Splendid Wine Dark Spl Ankle pUvxEqTibet El Slipper Pleasant Women's Stella Naturalista ND58 TBYrTUBlack US Hey 42 Mens Mistral Dude EU Size 9 Shoes Cxx8tq
Mesh Exercise Summer Dovaly Surf Water Aqua Breathable Gray Shoes Shoes Skin Men Air Flats Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Air Mesh Water Gray Aqua Shoes Surf Shoes Summer Men Exercise Flats Dovaly Skin Breathable 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
Shoes Flats Skin Dovaly Surf Water Exercise Gray Summer Shoes Mesh Aqua Air Breathable Men 3 0 0 0 85 Breathable Dovaly Men Summer Skin Surf Shoes Shoes Air Exercise Mesh Aqua Water Flats Gray 1 0 0 0 2
4 0 0 0 60 Flats Surf Skin Aqua Summer Breathable Water Mesh Dovaly Shoes Gray Exercise Air Shoes Men 2 0 0 0 2
5 3 4 Breathable Gray Summer Water Mesh Shoes Men Surf Air Aqua Shoes Flats Exercise Skin Dovaly 0 Flats Breathable Skin Dovaly Summer Mesh Water Exercise Shoes Surf Shoes Aqua Gray Men Air 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 Men Flats Air Surf Aqua Shoes Gray Shoes Water Skin Mesh Exercise Summer Dovaly Breathable 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; Aqua Flats Gray Water Shoes Breathable Shoes Air Men Skin Summer Surf Dovaly Exercise Mesh 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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