#statgen2024 — Public Fediverse posts

STATGEN 2024 talk
A Kernel-Based Neural Network for High-dimensional Risk Prediction on Massive Genetic Data
Qing Lu

Neural Network
Nonlinear
Non-additive

Kernel-Based Neural Network (KNN)
kernel matrics constructed based on the genetic variables.

Related preprint:
An Association Test Based on Kernel-Based Neural Networks for Complex Genetic Association Analysis
https://arxiv.org/abs/2312.06669

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
A Kernel-Based Neural Network for High-dimensional Risk Prediction on Massive Genetic Data
Qing Lu

Neural Network
Nonlinear
Non-additive

Kernel-Based Neural Network (KNN)
kernel matrics constructed based on the genetic variables.

Related preprint:
An Association Test Based on Kernel-Based Neural Networks for Complex Genetic Association Analysis
https://arxiv.org/abs/2312.06669

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
A Kernel-Based Neural Network for High-dimensional Risk Prediction on Massive Genetic Data
Qing Lu

Neural Network
Nonlinear
Non-additive

Kernel-Based Neural Network (KNN)
kernel matrics constructed based on the genetic variables.

Related preprint:
An Association Test Based on Kernel-Based Neural Networks for Complex Genetic Association Analysis
https://arxiv.org/abs/2312.06669

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
A Kernel-Based Neural Network for High-dimensional Risk Prediction on Massive Genetic Data
Qing Lu

Neural Network
Nonlinear
Non-additive

Kernel-Based Neural Network (KNN)
kernel matrics constructed based on the genetic variables.

Related preprint:
An Association Test Based on Kernel-Based Neural Networks for Complex Genetic Association Analysis
https://arxiv.org/abs/2312.06669

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Improved methods for empirical Bayes multivariate multiple testing and effect size estimation
Yunqi Yang

Empirical Bayes multivariate normal means (EBMNM) model [Urbut et al., 2019]

Allow for heterogeneous sharing of eQTLs in multiple tissues (e.g., some are shared across all tissues, some are shared only within brain tissues, etc.)

Truncated Eigenvalue Decomposition

udr: Ultimate Deconvolution in R
https://stephenslab.github.io/udr/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Improved methods for empirical Bayes multivariate multiple testing and effect size estimation
Yunqi Yang

Empirical Bayes multivariate normal means (EBMNM) model [Urbut et al., 2019]

Allow for heterogeneous sharing of eQTLs in multiple tissues (e.g., some are shared across all tissues, some are shared only within brain tissues, etc.)

Truncated Eigenvalue Decomposition

udr: Ultimate Deconvolution in R
https://stephenslab.github.io/udr/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Improved methods for empirical Bayes multivariate multiple testing and effect size estimation
Yunqi Yang

Empirical Bayes multivariate normal means (EBMNM) model [Urbut et al., 2019]

Allow for heterogeneous sharing of eQTLs in multiple tissues (e.g., some are shared across all tissues, some are shared only within brain tissues, etc.)

Truncated Eigenvalue Decomposition

udr: Ultimate Deconvolution in R
https://stephenslab.github.io/udr/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Improved methods for empirical Bayes multivariate multiple testing and effect size estimation
Yunqi Yang

Empirical Bayes multivariate normal means (EBMNM) model [Urbut et al., 2019]

Allow for heterogeneous sharing of eQTLs in multiple tissues (e.g., some are shared across all tissues, some are shared only within brain tissues, etc.)

Truncated Eigenvalue Decomposition

udr: Ultimate Deconvolution in R
https://stephenslab.github.io/udr/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
MultiSTAAR: A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies
Xihao Li

Functionally-informed Multi-Trait MultiSTAAR approach.

MultiSTAAR-O: Omnibus test
1. Burden
2. SKAT
3. ACAT-V

Li X et al. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. bioRxiv doi: 10.1101/2023.10.30.564764.

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
MultiSTAAR: A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies
Xihao Li

Functionally-informed Multi-Trait MultiSTAAR approach.

MultiSTAAR-O: Omnibus test
1. Burden
2. SKAT
3. ACAT-V

Li X et al. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. bioRxiv doi: 10.1101/2023.10.30.564764.

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
MultiSTAAR: A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies
Xihao Li

Functionally-informed Multi-Trait MultiSTAAR approach.

MultiSTAAR-O: Omnibus test
1. Burden
2. SKAT
3. ACAT-V

Li X et al. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. bioRxiv doi: 10.1101/2023.10.30.564764.

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
MultiSTAAR: A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies
Xihao Li

Functionally-informed Multi-Trait MultiSTAAR approach.

MultiSTAAR-O: Omnibus test
1. Burden
2. SKAT
3. ACAT-V

Li X et al. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. bioRxiv doi: 10.1101/2023.10.30.564764.

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Adventures in Human Genetics: Purpose, Serendipity, Innovation
Gonçalo Abecasis

"It is important to think carefully about what is the right question, and what are the right statistics. But there is a lot of opportunity in thinking about what is the best design to answer the question."

Goal
Understand disease
Treat
Predict disease
Prevent

Can learn from natural experiments in millions of people.

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Adventures in Human Genetics: Purpose, Serendipity, Innovation
Gonçalo Abecasis

"It is important to think carefully about what is the right question, and what are the right statistics. But there is a lot of opportunity in thinking about what is the best design to answer the question."

Goal
Understand disease
Treat
Predict disease
Prevent

Can learn from natural experiments in millions of people.

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Adventures in Human Genetics: Purpose, Serendipity, Innovation
Gonçalo Abecasis

"It is important to think carefully about what is the right question, and what are the right statistics. But there is a lot of opportunity in thinking about what is the best design to answer the question."

Goal
Understand disease
Treat
Predict disease
Prevent

Can learn from natural experiments in millions of people.

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Adventures in Human Genetics: Purpose, Serendipity, Innovation
Gonçalo Abecasis

"It is important to think carefully about what is the right question, and what are the right statistics. But there is a lot of opportunity in thinking about what is the best design to answer the question."

Goal
Understand disease
Treat
Predict disease
Prevent

Can learn from natural experiments in millions of people.

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Working towards Inclusivity in Genetic Studies: Estimating accurate population structure with Small Reference Sample Sizes
Souha Tifour

Arriaga-MacKenzie et al Summix: A method for detecting and adjusting for population structure in genetic summary data. Am J Hum Genet. 2021 Jul 1;108(7):1270-1282. doi: 10.1016/j.ajhg.2021.05.016.

Summix relies on reference populations, but what if the ref pop is small?

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Working towards Inclusivity in Genetic Studies: Estimating accurate population structure with Small Reference Sample Sizes
Souha Tifour

Arriaga-MacKenzie et al Summix: A method for detecting and adjusting for population structure in genetic summary data. Am J Hum Genet. 2021 Jul 1;108(7):1270-1282. doi: 10.1016/j.ajhg.2021.05.016.

Summix relies on reference populations, but what if the ref pop is small?

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Working towards Inclusivity in Genetic Studies: Estimating accurate population structure with Small Reference Sample Sizes
Souha Tifour

Arriaga-MacKenzie et al Summix: A method for detecting and adjusting for population structure in genetic summary data. Am J Hum Genet. 2021 Jul 1;108(7):1270-1282. doi: 10.1016/j.ajhg.2021.05.016.

Summix relies on reference populations, but what if the ref pop is small?

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Working towards Inclusivity in Genetic Studies: Estimating accurate population structure with Small Reference Sample Sizes
Souha Tifour

Arriaga-MacKenzie et al Summix: A method for detecting and adjusting for population structure in genetic summary data. Am J Hum Genet. 2021 Jul 1;108(7):1270-1282. doi: 10.1016/j.ajhg.2021.05.016.

Summix relies on reference populations, but what if the ref pop is small?

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Genotype prediction of 336,463 samples from public expression data
Afrooz Razi

recount3: uniformly processed RNA-seq
https://rna.recount.bio/

We developed a statistical model to predict genotypes from the Recount3 data

It has high prediction accuracy.

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Genotype prediction of 336,463 samples from public expression data
Afrooz Razi

recount3: uniformly processed RNA-seq
https://rna.recount.bio/

We developed a statistical model to predict genotypes from the Recount3 data

It has high prediction accuracy.

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Genotype prediction of 336,463 samples from public expression data
Afrooz Razi

recount3: uniformly processed RNA-seq
https://rna.recount.bio/

We developed a statistical model to predict genotypes from the Recount3 data

It has high prediction accuracy.

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Genotype prediction of 336,463 samples from public expression data
Afrooz Razi

recount3: uniformly processed RNA-seq
https://rna.recount.bio/

We developed a statistical model to predict genotypes from the Recount3 data

It has high prediction accuracy.

1/

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
BRCAPRO+BCRAT: extending a Mendelian breast cancer risk prediction model to include non-genetic risk factors
Zoe Guan

BRCAPRO: Mendelian model, genes

BCRAT: 1st family hx, hormonal risk factors, hx of benign disease

Combine these complementary models.

https://www.mdpi.com/2072-6694/15/4/1090

#STATGEN2024 #Genetics #BreastCancer #RiskPrediction #StatisticalGenetics

STATGEN 2024 talk
BRCAPRO+BCRAT: extending a Mendelian breast cancer risk prediction model to include non-genetic risk factors
Zoe Guan

BRCAPRO: Mendelian model, genes

BCRAT: 1st family hx, hormonal risk factors, hx of benign disease

Combine these complementary models.

https://www.mdpi.com/2072-6694/15/4/1090

#STATGEN2024 #Genetics #BreastCancer #RiskPrediction #StatisticalGenetics

STATGEN 2024 talk
BRCAPRO+BCRAT: extending a Mendelian breast cancer risk prediction model to include non-genetic risk factors
Zoe Guan

BRCAPRO: Mendelian model, genes

BCRAT: 1st family hx, hormonal risk factors, hx of benign disease

Combine these complementary models.

https://www.mdpi.com/2072-6694/15/4/1090

#STATGEN2024 #Genetics #BreastCancer #RiskPrediction #StatisticalGenetics

STATGEN 2024 talk
BRCAPRO+BCRAT: extending a Mendelian breast cancer risk prediction model to include non-genetic risk factors
Zoe Guan

BRCAPRO: Mendelian model, genes

BCRAT: 1st family hx, hormonal risk factors, hx of benign disease

Combine these complementary models.

https://www.mdpi.com/2072-6694/15/4/1090

#STATGEN2024 #Genetics #BreastCancer #RiskPrediction #StatisticalGenetics

STATGEN 2024 talk
Polygenic risk score analysis for multiethnic populations
Chris Amos

Polygenic Risk Scores (PRS)
* Inform re biological processes
* Identify some at higher risk
* Might motivate behavioral change

PRS could inform when to start screening.

"measles plot instead of a manhattan plot" - has excessive false positives all over the genome.

Lung cancer risk snp also is related to response to smoking cessation

1/

#STATGEN2024 #Polygenic #StatisticalGenetics #Genetics #PRS

STATGEN 2024 talk
Polygenic risk score analysis for multiethnic populations
Chris Amos

Polygenic Risk Scores (PRS)
* Inform re biological processes
* Identify some at higher risk
* Might motivate behavioral change

PRS could inform when to start screening.

"measles plot instead of a manhattan plot" - has excessive false positives all over the genome.

Lung cancer risk snp also is related to response to smoking cessation

1/

#STATGEN2024 #Polygenic #StatisticalGenetics #Genetics #PRS

STATGEN 2024 talk
Polygenic risk score analysis for multiethnic populations
Chris Amos

Polygenic Risk Scores (PRS)
* Inform re biological processes
* Identify some at higher risk
* Might motivate behavioral change

PRS could inform when to start screening.

"measles plot instead of a manhattan plot" - has excessive false positives all over the genome.

Lung cancer risk snp also is related to response to smoking cessation

1/

#STATGEN2024 #Polygenic #StatisticalGenetics #Genetics #PRS

STATGEN 2024 talk
Polygenic risk score analysis for multiethnic populations
Chris Amos

Polygenic Risk Scores (PRS)
* Inform re biological processes
* Identify some at higher risk
* Might motivate behavioral change

PRS could inform when to start screening.

"measles plot instead of a manhattan plot" - has excessive false positives all over the genome.

Lung cancer risk snp also is related to response to smoking cessation

1/

#STATGEN2024 #Polygenic #StatisticalGenetics #Genetics #PRS

STATGEN 2024 talk
Bayesian Meta-Analysis of Penetrance for Cancer Risk with Adjustment for Ascertainment Bias
Swati Biswas

Need accurate estimates of age-specific penetrance for cancer risk variants.
https://arxiv.org/abs/2304.01912

Heterogeneous studies w/ different measures of risk
Marabelli et al. Penetrance of ATM Gene Mutations in Breast Cancer: A Meta-Analysis of Different Measures of Risk. Genet Epidemiol. 2016 doi: 10.1002/gepi.21971

1/

#STATGEN2024 #Genetics #StatisticalGenetics #Pentrance

STATGEN 2024 talk
Bayesian Meta-Analysis of Penetrance for Cancer Risk with Adjustment for Ascertainment Bias
Swati Biswas

Need accurate estimates of age-specific penetrance for cancer risk variants.
https://arxiv.org/abs/2304.01912

Heterogeneous studies w/ different measures of risk
Marabelli et al. Penetrance of ATM Gene Mutations in Breast Cancer: A Meta-Analysis of Different Measures of Risk. Genet Epidemiol. 2016 doi: 10.1002/gepi.21971

1/

#STATGEN2024 #Genetics #StatisticalGenetics #Pentrance

STATGEN 2024 talk
Bayesian Meta-Analysis of Penetrance for Cancer Risk with Adjustment for Ascertainment Bias
Swati Biswas

Need accurate estimates of age-specific penetrance for cancer risk variants.
https://arxiv.org/abs/2304.01912

Heterogeneous studies w/ different measures of risk
Marabelli et al. Penetrance of ATM Gene Mutations in Breast Cancer: A Meta-Analysis of Different Measures of Risk. Genet Epidemiol. 2016 doi: 10.1002/gepi.21971

1/

#STATGEN2024 #Genetics #StatisticalGenetics #Pentrance

STATGEN 2024 talk
Bayesian Meta-Analysis of Penetrance for Cancer Risk with Adjustment for Ascertainment Bias
Swati Biswas

Need accurate estimates of age-specific penetrance for cancer risk variants.
https://arxiv.org/abs/2304.01912

Heterogeneous studies w/ different measures of risk
Marabelli et al. Penetrance of ATM Gene Mutations in Breast Cancer: A Meta-Analysis of Different Measures of Risk. Genet Epidemiol. 2016 doi: 10.1002/gepi.21971

1/

#STATGEN2024 #Genetics #StatisticalGenetics #Pentrance

STATGEN 2024 talk
Improving Genetic Risk Prediction with Genetic Architecture and Functional Annotations
Wei Jiang

Genome-wide Empirical Bayes to use both genetic architecture and functional annotations in a computationally efficient way.

* Summary-statistics-based
* No parameter tuning needed
* Has improved prediction accuracy over existing methods.

https://www.researchsquare.com/article/rs-3266942/v1

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Improving Genetic Risk Prediction with Genetic Architecture and Functional Annotations
Wei Jiang

Genome-wide Empirical Bayes to use both genetic architecture and functional annotations in a computationally efficient way.

* Summary-statistics-based
* No parameter tuning needed
* Has improved prediction accuracy over existing methods.

https://www.researchsquare.com/article/rs-3266942/v1

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Improving Genetic Risk Prediction with Genetic Architecture and Functional Annotations
Wei Jiang

Genome-wide Empirical Bayes to use both genetic architecture and functional annotations in a computationally efficient way.

* Summary-statistics-based
* No parameter tuning needed
* Has improved prediction accuracy over existing methods.

https://www.researchsquare.com/article/rs-3266942/v1

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Improving Genetic Risk Prediction with Genetic Architecture and Functional Annotations
Wei Jiang

Genome-wide Empirical Bayes to use both genetic architecture and functional annotations in a computationally efficient way.

* Summary-statistics-based
* No parameter tuning needed
* Has improved prediction accuracy over existing methods.

https://www.researchsquare.com/article/rs-3266942/v1

#STATGEN2024 #Genetics #StatisticalGenetics

STATGEN 2024 talk
Novel Methods for Estimating Risk Parameters Associated with Polygenic Scores Using Case-Parent Trio Designs
Ziqiao Wang

Estimates of SNP effect sizes can be biased due to
* Population stratification
* Assortative mating

Prior method
PRS TDT (pTDT) (Weiner et al., Nat Genet 2017)

Goal
To develop a joint model that is flexible and robust

Assume family PGS ~ multivariate normal distribution w/ family-specfic mean & var

1/

#Genetics #StatisticalGenetics #STATGEN2024

STATGEN 2024 talk
Novel Methods for Estimating Risk Parameters Associated with Polygenic Scores Using Case-Parent Trio Designs
Ziqiao Wang

Estimates of SNP effect sizes can be biased due to
* Population stratification
* Assortative mating

Prior method
PRS TDT (pTDT) (Weiner et al., Nat Genet 2017)

Goal
To develop a joint model that is flexible and robust

Assume family PGS ~ multivariate normal distribution w/ family-specfic mean & var

1/

#Genetics #StatisticalGenetics #STATGEN2024

STATGEN 2024 talk
Novel Methods for Estimating Risk Parameters Associated with Polygenic Scores Using Case-Parent Trio Designs
Ziqiao Wang

Estimates of SNP effect sizes can be biased due to
* Population stratification
* Assortative mating

Prior method
PRS TDT (pTDT) (Weiner et al., Nat Genet 2017)

Goal
To develop a joint model that is flexible and robust

Assume family PGS ~ multivariate normal distribution w/ family-specfic mean & var

1/

#Genetics #StatisticalGenetics #STATGEN2024

STATGEN 2024 talk
Novel Methods for Estimating Risk Parameters Associated with Polygenic Scores Using Case-Parent Trio Designs
Ziqiao Wang

Estimates of SNP effect sizes can be biased due to
* Population stratification
* Assortative mating

Prior method
PRS TDT (pTDT) (Weiner et al., Nat Genet 2017)

Goal
To develop a joint model that is flexible and robust

Assume family PGS ~ multivariate normal distribution w/ family-specfic mean & var

1/

#Genetics #StatisticalGenetics #STATGEN2024

STATGEN 2024 talk
Genetic Associations with Dynamic Placental Proteins Identify Biomarkers for Hypertension in Pregnancy
Qi Yan

GWAS of nine placental proteins from first- and second-trimester serum. Found associations with ADAM-12, VEGF, and sFlt-1.

Mendelian Randomization gives evidence for causal relationships between placental proteins, particularly ADAM-12 and PE and gestational hypertension.

#Genetics #PreEclampsia #STATGEN2024

STATGEN 2024 talk
Linking variants to gene networks with multivariate association approaches
Xuanyao Liu

Detecting trans-eQTLs is challenging
- Small trans- effects
- Multiple-testing correction
- Overwhelmed by false positives

Trans-PCO method

PCO = PC-based omnibus test

https://github.com/liliw-w/Trans

1/

#STATGEN2024 #StatisticalGenetics #Genetics

STATGEN 2024 talk
Linking variants to gene networks with multivariate association approaches
Xuanyao Liu

Detecting trans-eQTLs is challenging
- Small trans- effects
- Multiple-testing correction
- Overwhelmed by false positives

Trans-PCO method

PCO = PC-based omnibus test

https://github.com/liliw-w/Trans

1/

#STATGEN2024 #StatisticalGenetics #Genetics

STATGEN 2024 talk
Linking variants to gene networks with multivariate association approaches
Xuanyao Liu

Detecting trans-eQTLs is challenging
- Small trans- effects
- Multiple-testing correction
- Overwhelmed by false positives

Trans-PCO method

PCO = PC-based omnibus test

https://github.com/liliw-w/Trans

1/

#STATGEN2024 #StatisticalGenetics #Genetics

STATGEN 2024 talk
Linking variants to gene networks with multivariate association approaches
Xuanyao Liu

Detecting trans-eQTLs is challenging
- Small trans- effects
- Multiple-testing correction
- Overwhelmed by false positives

Trans-PCO method

PCO = PC-based omnibus test

https://github.com/liliw-w/Trans

1/

#STATGEN2024 #StatisticalGenetics #Genetics

STATGEN 2024 talk
Localizing Rare-Variant Association Regions via Multiple Testing Embedded in an Aggregation Tree
Jichun Xie

Which variants
* Gene region
* Sliding window (fixed size)
* Varying window

DYNamic Aggregation TEsting (DYNATE) algorithm

"DYNATE dynamically and hierarchically aggregates smaller genomic regions into larger ones"

https://cran.r-project.org/package=DYNATE

1/

#STATGEN2024 #Genetics #StatisticalGenetics #RareVariants