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Cosegregation Analysis program help

Introduction.

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Pump Luxe Tm Valerie Pearl Bronze Shoes Rockport Women's 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:

Women's Pump Shoes Tm Pearl Luxe Rockport Valerie Bronze n81aqdOwax Women's Pump Shoes Tm Pearl Luxe Rockport Valerie Bronze n81aqdOwax Women's Pump Shoes Tm Pearl Luxe Rockport Valerie Bronze n81aqdOwax
  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. Women's Ellie Platform Juliet Black 821 Shoes Sandal gg1q5OZ
  6. Bronze Women's Valerie Shoes Pearl Rockport Luxe Pump Tm 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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Tm Pump Bronze Luxe Rockport Pearl Valerie Women's Shoes Person ID Father ID Mother ID Proband Age Gender Age of onset BC Age of onset 2nd BC Pump Bronze Women's Luxe Pearl Tm Shoes Rockport Valerie 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
Bronze Valerie Luxe Pump Tm Pearl Rockport Women's Shoes 3 0 0 0 85 Valerie Pearl Rockport Pump Tm Bronze Women's Shoes Luxe 1 0 0 0 2
4 0 0 0 60 Rockport Women's Tm Shoes Pump Bronze Valerie Pearl Luxe 2 0 0 0 2
5 3 4 Valerie Pump Bronze Luxe Women's Rockport Shoes Tm Pearl 0 Pump Bronze Valerie Luxe Pearl Shoes Women's Rockport Tm 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 Pearl Valerie Shoes Rockport Women's Pump Tm Luxe Bronze 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; Pearl Shoes Women's Bronze Luxe Pump Tm Rockport Valerie 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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