NG00171 – Population Structure in LASI-DAD

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Description

This dataset includes summary statistics characterizing genetic population structure of individuals in the LASI-DAD cohort. This includes estimates of population admixture and founder events, including segments of Neanderthal and Denisovan ancestry and regions of homozygosity in India. We used the whole genome sequences for 2,762 individuals part of the LASI-DAD sample set snd10033. Sequencing depth information is provided for 2,712 individuals as a preliminary metric of data quality. Of the total sample pool, 2,679 samples passed quality control filters. For these individuals, we provide information about sequencing depth for each individual, ancestry proportions measured using population genetics tool – qpAdm, runs of homozygosity inferred using PLINK and estimates of Neanderthal and Denisovan ancestry based on hmmix. Details of the analysis and methods are described in the biorxiv preprint (bioRxiv 2024.02.15.580575, doi: https://doi.org/10.1101/2024.02.15.580575)

To obtain subject ID mapping between LASI-DAD datasets, please contact Jinkook Lee (jinkookl@usc.edu) or apply for data access on the LASI-DAD website.

Sample Summary per Data Type

Sample Set	Accession	Data Type	Number of Samples
Population Structure in LASI-DAD	snd10117	Population Structure Summary Statistics	2,712

Available Filesets

Name	Accession	Latest Release	Description
LASI-DAD Population Structure	fsa000126	NG00171	Population Structure Summary Statistics

View the File Manifest for a full list of files released in this dataset.

A total of 2,762 LASI-DAD participants, including 22 trios (mother-father-child), were sequenced at MedGenome, Inc. (Bangalore, India) at an average read depth of 30. Individuals were sampled from 18 different states across India, with median sample size of 157 individuals per state. The raw whole genome sequences were sent to the Genome Center for Alzheimer’s Disease (GCAD) at the University of Pennsylvania for joint calling and quality control. A total of 2,679 samples and 73.2 million autosomal bi-allelic variants passed quality control filters, including 67.1 million single nucleotide variants (SNVs) and 6.04 million insertion-deletions (indels).The dataset includes individuals born in 23 different states, speaking at least 26 different languages, from both rural (63%) and urban (37%) areas, and belonging to various caste groups as recognized by the Indian government: 4% from Scheduled Tribes, 18% from Scheduled Castes, and 44% from other backward class (OBC). Nearly equal numbers of males and females were recruited in the study constituting 52% of females. For many analyses, individuals were categorized, based on their birth location, into six major geographic regions: North (n=555), West (n=385), Central (n=373), South (n=715), North-East (n=73), and East (n=530). Most analysis in this dataset are preformed on 2,620 individuals that passed quality control checks and excludes first-degree relatives.

Sample Set	Accession Number	Number of Subjects	Number of Samples
Population Structure in LASI-DAD	snd10117	1	2,712

NG00171 – Population Structure in LASI-DAD

Overview

Description

Sample Summary per Data Type

Available Filesets

Sample information

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Acknowledgement

Acknowledgment statement for any data distributed by NIAGADS:

For investigators using any data from this dataset:

For investigators using The Diagnostic Assessment of Dementia for the Longitudinal Aging Study of India (LASI-DAD) (sa000019) data:

Related Publications

Total number of samples: 0