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BayesMendel Update Log

Version 2.1-8-1 11/22/21
1. Fixed bug that affected BRCAPRO when the proband was White and had breast cancer.
2. Added default seed (42).
3. Fixed bug that affected MMRPRO when the proband had an age that was NA (either AgeColon or AgeEndometrium).

 

Version 2.1-8  08/24/2021
1. Added BRCAPANCpro (combination of BRCAPRO and PancPRO to include breast, ovarian, and pancreatic cancer, and BRCA1, BRCA2, and a hypothetical PANC gene that increases susceptibility to pancreatic cancer).
2. Removed association between male breast cancer and BRCA1.
3. Removed test order for germline testing
4. Changed sensitivity and specificity parameters for germline testing to 1.
5. Changed the default future risk prediction to crude (from net).
6. Changed the imputeRelatives argument to FALSE by default
7. Changed our method of calculating future risk of contralateral breast cancer.
8. Fixed bug in LyteSimple.
9. We return an error if the current age from the AgeX variables is inconsistent with AgeDeath.
 

Version 2.1-7 09/09/2020
1. Updated LFSpro to version 2.0.0
2. Added brcaproPlusBCRAT (combination of BRCAPRO and BCRAT where we use relative risks from BCRAT to modify the BRCAPRO penetrances).
3. Updated the age imputation (ImputeAge function) to allow for imputing caner ages based on intervals. Users can provide columns indicating lower and upper bounds for the imputed cancer ages. Also, imputed cancer ages are now bounded above by the current age. Some other minor bugs were fixed in this function.
4. Updated SEER race-specific breast cancer penetrances and hazards of death from other causes to be based on only invasive breast cancer, and not invasive or DCIS.

Version 2.1-6 01/22/2020
1. New female breast cancer and ovarian cancer penetrances based on Chen, Bae et al.
2. New colorectal and endometrial cancer penetrances based on Wang et al.
3. Updated non-carrier penetrances for male breast cancer, pancreatic cancer, and melanoma using estimates from SEER, version 6.7.7. Also used these SEER estimates to update race-specific non-carrier penetrances for all cancers.
4. Male mastectomies now affect future risk.
5. Fixed bug in the way MSI information is incorporated.
 

Version 2.1-5 06/14/2019
1. Re-estimated all penetrance ages 1-94. 
2. Added differentiation between crude/net penetrance for BRCAPRO, MMRpro, MelaPRO, PancPRO. 
3. Fixed imputations for MMRpro, MelaPRO, PancPRO.
4. Added race specific baseline penetrance for MMRpro, MelaPRO, PancPRO.
5. Updated baseline penetrance from SEER DevCan 6.7.5.
6. Fix bug in TestContributions, affects families who have multiple people test positive.
7. Remove PREMM from R package.
8. User-inputted germline/marker testing or mastectomy/oophorectomy information now overrides the information in the columns of the pedigree data frame.
 

Version 2.1-4, 3/30/2018
1. Added ‘myseed’ as a parameter to helper functions brcaparams(), mmrparams(), pancparams() and melaparams() to set the seed for multiple imputation of missing disease age
2.  Updated the way future risk calculations are performed with updated dens2haz.cs function.
3.  Age of menopause considered for future risk calculations for those who have had oophorectomy has been lowered from age 59 to age 44.
4.  Prevalence of BRCA1 and BRCA2 mutations for Ashkenazi Jewish family members has been updated (increased from 0.00609756097560976 and 0.00679723502304147 to 0.01366243 and 0.01168798, respectively.

 

Older versions of the BayesMendel R package are described below and available by email request. Please send your name, institution, and package version number desired to bmendel@jimmy.harvard.edu

 

 

 

Version 2.1-3, 3/31/16

  1. Adding imputeAge and imputeRelatives option to all models

Version 2.1-2, 9/8/15

  1. New model LFSpro now included
  2. Lyte-Simple imputation approach now added for all models
  3. Lyte-Plus also now extended to all models
  4. Twins can now be included in all models.

Version 2.1-1, 2/23/2015

  1. Corrected an error in peelingRC related to handling of family member-specific ethnicity
  2. Allow for missing age inputs (NA) for all models

Version 2.1, 10/3/2014

  1. Added MakeRelationship back to the package so facilitate use of PREMM and age imputation in the BayesMendel models.
  2. Added the PREMM model to the package.
  3. Fixed a few plotting problems in BayesMendel.R
  4. Fixed a bug in CensorAtIntervention.R
  5. Changed the way twins are handled. Now the LIK is collapsed before entered into peeling instead of collapsing twins in CheckFamStructure.
  6. Unknown ages are now being imputed via the helper function “ImputeAge”
  7. Default sensitivity of BRCA testing has been updated to 99% to reflect 2012 estimates from Myriad.
  8. Added the data object “BrOvJointDsn.RData” to the package to assist with age imputation when a family member is affected with both breast and ovarian cancers but the ages of diagnosis are unknown.

Version 2.0-9, 3/24/14

  1. Fixed a bug when families would have multiple interventions
  2. The peeling algorithm returns NA when it cannot calculate a probability

Version 2.0-813, 5/28/13

  1. Fixed BRCAPRO bug when pedigrees had multiple family members with interventions.

Version 2.0-812, 5/28/13

  1. Fixed BRCAPRO bug when predicting future risk predictions when last listed family member was counselee.
  2. Fixed BRCAPRO bug when "ethnic" field is read in by R software as a "factor".
  3. The BRCAPRO hazard ratio for ovarian cancer following mastectomy is updated to be uninformative.
  4. In BRCAPRO, if a family has at least one AJ family member, the ethnic field is set to AJ for any members with unknown ethnicity. Otherwise missing ethnicity is set to nonAJ.

Version 2.0-81, 3/20/13

  1. The peeling algorithm has been converted to c-code to improve computation time without changing estimates.

Version 2.0-8, 1/29/13 **latest version**

  1. BRCAPRO has been re-calibrated and improved with updated penetrances for contralateral breast cancer.
  2. Package now allows for input on ethnicity for each family member, in order to better characterize families containing more than one ethnic groups, each of which may present different allele frequencies for the mutations of interest.
  3. Mastectomy as an intervention has been added to BRCAPRO.
  4. Improved the error message returned when there is a problem with the Twins input.

Version 2.0-7, 3/06/12

  1. Package now requires kinship2, as kinship was retired from CRAN on 3/14/12
  2. Fixed a bug in CheckFamStructure when a pair of twins and no other relatives are included in the pedigree.
  3. Updated default sensitivity parameters for BRCA1/2 testing to 95%.

Version 2.0-6, 10/20/11

  1. Her-2 status added to brcapro
  2. Other marker parameters have been updated
  3. Identical twins can be put into the pedigree
  4. Wenyi fixed a half-sib bug and Amanda fixed a bug related to future risk when oophorectomy was done on the proband.

Version 2.0-5, 10/8/10

  1. Post-oophorectomy hazard ratios have been updated to reflect Domchek et al, JAMA 2010 and have taken away protective effect after menopause (HR set to 1.0 for women aged > 60).
  2. Wenyi fixed two bugs related to half-siblings.

Version 2.0-4, 2/12/10

  1. Melapro added to the package

Version 2.0-3, 7/22/09

  1. BRCAPRO now outputs future risk of contralateral breast cancer for a counselee who has a diagnosed primary breast cancer.
  2. For all models, if the counselee already has a diagnosed cancer (contralateral breast, ovarian, pancreas, colon, endometrial), future risk is no longer output.

Version 2.0-2, 3/17/09

  1. BRCAPRO now considers race/ethnicity

Version 2.0, 4/20/08

  1. Pedigrees of any size can be included in the model

Version 1.4-3, 4/10/07

  1. Pancreas cancer model, PancPRO, added to the package

Version 1.4-2, 10/24/06

  1. MMRpro and brcapro prediction algorithm uses hazard function and accounts for death from other causes.
  2. calc.future.risk function added.
  3. make.BM.object function removed.
  4. death.othercauses data set added.
  5. MMRpro and brcapro output objects of class BayesMendel for use in generic plot function.

Version 1.4-1, 9/12/06

  1. Changed all referenes of 'crcapro' to 'MMRpro'
  2. Incorporated a new 3-gene version of 'MMRpro', Ngene. Ngene completely replaces aveG and margene for both brcapro and MMRpro.
  3. Moved parameter specification part of MMRpro to MMRparams
  4. Removed 'cancerrisk' and 'summary.cancerrisk' - now incorporated into 'brcapro'
  5. Note the rows and columns of the posterior probability matrix for brcapro have been switched.
  6. New .Rdata files 'MMRpenet' and 'MMR.fam' replace 'HNPCCpenet.2004' and 'crca.fam'.
  7. Output for brcapro and MMRpro is now in list format
  8. Function 'makeBMobject' added for enabling use of generic plot function to plot pedigree structure

Version 1.3-2, 7/20/06

  1. Added generic 'plot' option to display pedigree structure and probabilities

Version 1.3-1, 3/30/06

  1. Updated penetrance estimates for breast and ovarian cancers
  2. Oophorectomy history can be included in the model
  3. Molecular marker information can be included in the model

Version 1.2-5, 9/28/05

  1. Fixed a typo in brcapro.R (It does not affect the calcuation though)
  2. Added a patch (margenerec.c) so that BayesMendel can handle models with recessive mode of inheritance. See the help file for aveG(), which can now be specified to do recessive calculations.
  3. Replace Australian.R with LAMBDA.R, use the help file for LAMBDA() for details.

Version 1.2-4, 6/22/05

  1. Fixed a bug in cancerrisk.R

Version 1.2-3, 2/1/05

  1. Updated BRCApenet.AJ.2004 and BRCApenet.nonAJ.2004

Version 1.2-2, 11/18/04

  1. Added in MakeRelationship.R
  2. Added in BRCApenet.Italian.RData, the BRCA penetrance object for the Italian population (Marroni 2004)
  3. Added in Australian.R (Apicella 2003)
  4. Improved the documentations

Version 1.2-1, 9/8/04

  1. Added in new BRCA penetrances for AJ and nonAJ (Chen 2004) BRCApenet.AJ.2004 BRCApenet.nonAJ.2004
  2. Updated HNPCCpenetrance HNPCCpenet.2004
  3. Impoved documentation for the penetrance objects

Version 1.1-15, 8/30/04

  1. Improved output description (documentation)
  2. Fixed the problem with endometrial cancer in CRCAPRO
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References:
Chen S, Iversen ES, Friebel Tara, Finkelstein D, Weber BL, Eisen A, Peterson LE, Schildkraut JM, Isaacs C, Peshkin BN, Corio C, Leondaridis L, Tomlinson G, Amos CI, Strong LC, Berry DA, Dutson D, Kerber R, Euhus DM, Parmigiani G. Comprehensive Evaluation of Breast and Ovarian Cancer Risks Associated with BRCA1 and BRCA2 Mutations. (in progress) 2004

Marroni, F., Aretini, P., D'Andrea, E., Caligo, M.A., Cortesi, L., Viel, A., Ricevuto, E., Montagna, M., Cipollini, G., Federico, M. et al. (2004) Penetrances of breast and ovarian cancer in a large series of families tested for BRCA1/2 mutations. Eur J Hum Genet, 12, 899-906.

Apicella C, Andrews L, Hodgson SV, Fisher SA, Lewis CM, Soloman E, Tucker K, Friedlander M, Bankier A, Southey MC, Venter DJ, Hopper JL. Log odds of carrying an Ancestral Mutation in BRCA1 or BRCA2 for a Defined personal and family history in an Ashkenazi Jewish woman (LAMBDA). Breast Cancer Research 5(6): R206-216.

Hopper JL, Jenkins MA. Modeling the probability that Ashkenazi Jewish women carry a founder mutation in BRCA1 or BRCA2. American Journal of Human Genetics 1999, 65: 1771-1775.