Modeling the effect of Leigh syndrome-associated mutations using human cerebral organoids

Authors: Alejandra I. Romero-Morales, Anuj Rastogi, Hoor Temuri, Megan Rasmussen, Gregory Scott McElroy, Lawrence Hsu, Paula M. Almonacid, Bryan Millis, Navdeep S Chandel, Jean-Philippe Cartailler and Vivian Gama

Please cite: TBD

Data and metadata

All raw data has been deposited via GEO:

• SRA accession: PRJNA626388 (A reviewer link is available upon request)
• Release date: 2020-08-01 (tentative until manuscript is accepted for publication)

Source code

Variant analysis (deliverable 1)

01-SnpEff:

Input:

SNP: Deliverable-1/01-Preprocessing/Input/all.samples.filtered.snp.nonsynonymous.ann.vcf

Indel: Deliverable-1/01-Preprocesing/Input/all.samples.filtered.indel.nonsynonymous.ann.vcf

Code:

Used snpSift to extract the columns in both the SNP and indel VCF files before downstream analysis:

SNP file:

java -jar SnpSift.jar extractFields all.samples.filtered.snp.nonsynonymous.ann.vcf CHROM POS ID REF ALT QUAL "ANN[0].ALLELE" "ANN[0].EFFECT" "ANN[0].IMPACT" "ANN[0].GENE" "ANN[0].GENEID" "ANN[0].FEATURE" "ANN[0].FEATUREID" "GEN[GM01503].GT" "GEN[GM03672].GT" "GEN[GM13411].GT" > snpEff_processed.vcf

Indel file:

java -jar SnpSift.jar extractFields all.samples.filtered.indel.nonsynonymous.ann.vcf CHROM POS ID REF ALT QUAL "ANN[0].ALLELE" "ANN[0].EFFECT" "ANN[0].IMPACT" "ANN[0].GENE" "ANN[0].GENEID" "ANN[0].FEATURE" "ANN[0].FEATUREID" "GEN[GM01503].GT" "GEN[GM03672].GT" "GEN[GM13411].GT" > snpEff_processed_indel.vcf

Output:

SNP: Deliverable-1/01-Preprocessing/Output/snpEff_processed.vcf Indel: Deliverable-1/01-Preprocessing/Output/snpEff_processed_indel.vcf

02-GeneWiz_reproduce

Input:

Deliverable-1/02-GeneWiz_reproduce/Input/snpEff_processed.vcf Deliverable-1/02-GeneWiz_reproduce/Input/snpEff_processed_indel.vcf Deliverable-1/02-GeneWiz_reproduce/Input/ensembl_to_uniprot

Code:

Run Deliverable-1/02-GeneWiz_reproduce/Src/snpeff_reproduce_GeneWiz_Variant_Hit.R

Output:

Location: Deliverable-1/02-GeneWiz_reproduce/Output/

Items:

genewiz_report_snpeff_indel_Gr37.xlsx and ` genewiz_report_snpeff_snp_Gr37.xlsx` - reproduction of the GeneWiz report from raw data

snpeff_indel_Gr37.xlsx and snpeff_snp_Gr37.xlsx - additional information CDS added on top of the genewiz report

snpeff-gr37-indel-full.csv and snpeff-gr37-snp-full.csv- Input data generated for other deliverable.

Figure 1B (Indel circular plot)

Input:

Deliverable-2/01-snp-indel-circular-plot/Input/snpeff-gr37-indel-full.csv

Code:

1. Run Deliverable-2/01-snp-indel-circular-plot/Src/biocircos.R
2. Save plots.

Note - three genes manually using Inkscape 0.92. Ticks have been drawn in.

Gene Name	chrom	end	start
AC074212.3	19	46236509	46267792
AC012123.1	18	30354376	30349758
AC096644.1	1	220608023	220603286

Output:

Location: Deliverable-2/01-snp-indel-circular-plot/Output/

SVG formatted circular plot:indel_circosplot_final.svg

Figure 1C (SNP circular plot)

Input:

Deliverable-2/01-snp-indel-circular-plot/Input/snpeff-gr37-snp-full.csv

Code:

1. Run Deliverable-2/01-snp-indel-circular-plot/Src/biocircos.R
2. Save plots.

Output:

Location: Deliverable-2/01-snp-indel-circular-plot/Output/

SVG formatted circular plot: snp_circosplot_final.svg

Figure 1D (Mitochondrial circular plot)

Input:

Deliverable-2/02-snp-circular-chromosome-mito-plot/Input/snpeff-gr37-snp-full.csv

Deliverable-2/02-snp-circular-chromosome-mito-plot/Input/color_ref.csv

Deliverable-2/02-snp-circular-chromosome-mito-plot/Input/crossref.csv

Code:

1. Run Deliverable-2/02-snp-circular-chromosome-mito-plot/Src/mito_circos.R
2. Save plots

Output:

Location: Deliverable-2/02-snp-circular-chromosome-mito-plot/Output/

SVG formatted circular plot: mito_circoplot.svg