OSCR

A frameshift variant in FAM129C contributes to achalasia through B cell responses against the GABA<sub>A</sub> receptor.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches
  1. [1] § Methods › Whole-genome sequencing (WGS) ↔ recessive_denovo_LOF_pipeline.sh, lines 51–114 · score 0.74 · splice site, LoF variants, de novo, nonsense, bp, gnomAD
  2. [2] § Results › Identification of a FAM129C frameshift variant associated with achalasia ↔ recessive_denovo_LOF_pipeline.sh, lines 51–114 · score 0.58 · de novo variant, frameshift variant, bp, chr, gnomAD, recessive

Paper

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The authors' code

Shell · 114 lines · 5.2 KB · no license · 2 matches

  1. #!/bin/bash
  2. # Pipeline: Recessive + De novo LOF variants (AF < 0.01)
  4. set -euo pipefail
  6. # ==================== CONFIGURATION (EDIT THESE) ====================
  7. PROJECT_DIR=/path/to/your/project
  8. DATA_DIR=/path/to/data
  9. CHR_LIST=$(ls $PROJECT_DIR/data/ | grep tbi | awk -F. '{print $2}' | grep -v X | tail -n 28)
  11. # Subdirectories (relative to PROJECT_DIR)
  12. SAMPLE_LIST="$PROJECT_DIR/AC/data_sample/AC_sample.list"
  13. COLNAME_FILE="$PROJECT_DIR/AC/data_sample/colname"
  14. FAMILY_INPUT="$PROJECT_DIR/AC/data_sample/AC_family.input"
  15. FILTER_RESULT_DIR="$PROJECT_DIR/randomf/filter_result"
  16. GNOMAD_INPUT_DIR="$PROJECT_DIR/AC/get_AF/input"
  17. DENOVO_REC_RESULT_DIR="$PROJECT_DIR/AC/denovo_rec/result"
  18. PASS_VAR_DIR="$PROJECT_DIR/pass_var"
  19. RAREVAR_DIR="$PROJECT_DIR/rarevar"
  20. ANNO_DIR="$PROJECT_DIR/anno"
  21. AC_DATA_VCF_DIR="$PROJECT_DIR/AC/data_vcf"
  22. AC_DATA_GT_DIR="$PROJECT_DIR/AC/data_GT"
  23. AC_PASS_VID_DIR="$PROJECT_DIR/AC/pass_vid"
  24. AC_RAREVAR_DIR="$PROJECT_DIR/AC/rarevar"
  25. PYTHON_SCRIPT="$PROJECT_DIR/AC/denovo_rec/GT_denovo_rec.py"
  26. DNM_PASS_LIST="$PROJECT_DIR/AC/denovo/vid_dnm.pass.list"
  28. # ==================== 1. Extract genotypes ====================
  29. for CHR in $CHR_LIST; do
  30. bcftools view -S $SAMPLE_LIST \
  31. $DATA_DIR/vcf/ACH_CHD_GRCh37.${CHR}.dn.vcf.gz \
  32. -c1 -Oz -o $AC_DATA_VCF_DIR/AC_GRCh37.${CHR}.dn.nofilter.vcf.gz
  33. tabix -p vcf $AC_DATA_VCF_DIR/AC_GRCh37.${CHR}.dn.nofilter.vcf.gz
  35. bcftools query -f "%ID[\t%GT]\n" $AC_DATA_VCF_DIR/AC_GRCh37.${CHR}.dn.nofilter.vcf.gz | \
  36. grep -v '\*' | cat $COLNAME_FILE - > $AC_DATA_GT_DIR/AC_GRCh37.${CHR}.GT.nofilter.txt
  37. done
  39. # ==================== 2. Keep QC-passed variants ====================
  40. for CHR in $CHR_LIST; do
  41. awk '{if($2==1) print $1}' $FILTER_RESULT_DIR/${CHR}.tsv > $PASS_VAR_DIR/${CHR}_pass_vid.tsv
  42. done
  44. for CHR in $CHR_LIST; do
  45. awk 'NR==FNR{a[$1]=$0;} NR>FNR && a[$1] {print a[$1]"\t"$0}' \
  46. $DENOVO_REC_RESULT_DIR/AC_GRCh37.${CHR}_rec_denovo.nofilter.txt \
  47. $PASS_VAR_DIR/${CHR}_pass_vid.tsv | \
  48. awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7}' > $AC_PASS_VID_DIR/AC_GRCh37.${CHR}_rec_denovo.pass.txt
  49. done
  51. # ==================== 3. Keep rare variants (AF < 0.01) ====================
  52. for CHR in $CHR_LIST; do
  53. awk '{if($5 < 0.01) print $0}' $GNOMAD_INPUT_DIR/ACH_CHD_GRCh37.${CHR}.gnomad.txt > $RAREVAR_DIR/AC_CHD_${CHR}_rarevar.txt
  54. done
  56. for CHR in $CHR_LIST; do
  57. awk 'NR==FNR{a[$1]=$0;} NR>FNR && a[$1] {print a[$1]"\t"$0}' \
  58. $AC_PASS_VID_DIR/AC_GRCh37.${CHR}_rec_denovo.pass.txt \
  59. $RAREVAR_DIR/AC_CHD_${CHR}_rarevar.txt > $AC_RAREVAR_DIR/AC_CHD_${CHR}_rec_denovo.pass_rarevar.txt
  60. done
  62. # ==================== 4. Annotate (exclude intergenic) ====================
  63. for CHR in $CHR_LIST; do
  64. bcftools query -f '%ID\t%INFO/CSQ' $DATA_DIR/vcfqc/ACH_CHD_GRCh37.${CHR}.anno3.vcf.gz | \
  65. grep -v intergenic_variant | \
  66. awk -F'|' '{print $1"\t"$2"\t"$3"\t"$4}' > $ANNO_DIR/${CHR}.anno.txt
  67. done
  69. # Merge rare variants with annotations (adjust column numbers if needed)
  70. for CHR in $CHR_LIST; do
  71. awk 'NR==FNR{a[$1]=$0;} NR>FNR && a[$1] {print a[$1]"\t"$0}' \
  72. $AC_RAREVAR_DIR/AC_CHD_${CHR}_rec_denovo.pass_rarevar.txt \
  73. $ANNO_DIR/${CHR}.anno.txt | \
  74. awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$11"\t"$12"\t"$15"\t"$16"\t"$17}' >> $PROJECT_DIR/AC_all_rare_AF0.01_annotated.tsv
  75. done
  77. # ==================== 5. Identify recessive & de novo patterns (Python) ====================
  78. for CHR in $CHR_LIST; do
  79. python $PYTHON_SCRIPT \
  80. $FAMILY_INPUT \
  81. $AC_DATA_GT_DIR/AC_GRCh37.${CHR}.GT.nofilter.txt \
  82. $DENOVO_REC_RESULT_DIR/AC_GRCh37.${CHR}_rec_denovo.nofilter.txt
  83. done
  84. # Merge de novo and recessive pass list with annotations
  85. for CHR in $CHR_LIST; do
  86. awk 'NR==FNR{a[$1]=$0;} NR>FNR && a[$1] {print a[$1]"\t"$0}' \
  87. $DENOVO_REC_RESULT_DIR/AC_GRCh37.${CHR}_rec_denovo.nofilter.txt \
  88. $PROJECT_DIR/AC_all_rare_AF0.01_annotated.tsv >> $PROJECT_DIR/AC_rec.pass_coding_AF0.01.tsv
  89. done
  91. awk 'NR==FNR{a[$1]=$0;} NR>FNR && a[$1] {print a[$1]"\t"$0}' \
  92. $DNM_PASS_LIST \
  93. $PROJECT_DIR/AC_all_rare_AF0.01_annotated.tsv > $PROJECT_DIR/AC_dnm.pass_coding_AF0.01.tsv
  95. # ============= 6. Filter LOF variants （nonsense, frameshift, and splice-site (±2 bp) mutations.）==========
  96. LOF_OUTPUT="$PROJECT_DIR/AC_LOF_rare_AF0.01_rec_denovo.tsv"
  97. # Column assumptions: $2 = rec (recessive), $10 = Consequence (adjust if needed)
  98. awk 'BEGIN{OFS="\t"; print "#LOF_variants\tAF<0.01\trecessive_or_denovo"}
  99. NR==1 {print $0, "LOF_type"}
  100. NR>1 {
  101. lof=0; reason="";
  102. if($9 ~ /stop_gained|frameshift_variant|splice_acceptor_variant|splice_donor_variant/) {lof=1; reason=$9}
  103. # De novo variants are already in this file (from DNM list)
  104. if(lof==1) print $0, reason;
  105. }' $PROJECT_DIR/AC_dnm.pass_coding_AF0.01.tsv > $LOF_OUTPUT
  107. awk 'BEGIN{OFS="\t"; print "#LOF_variants\tAF<0.01\trecessive_or_denovo"}
  108. NR==1 {print $0, "LOF_type"}
  109. NR>1 {
  110. lof=0; reason="";
  111. if($9 ~ /stop_gained|frameshift_variant|splice_acceptor_variant|splice_donor_variant/) {lof=1; reason=$9}
  112. # Recessive: $2 not empty and not ";"
  113. if(lof==1 && $2 !~ /^;$/ && $2 != "") print $0, reason;
  114. }' $PROJECT_DIR/AC_rec.pass_coding_AF0.01.tsv >> $LOF_OUTPUT

recessive_denovo_LOF_pipeline.sh at commit 6a18be9, no license · at the source

Overview

Authors: Xiao-Qing Li1,2, Xin-Yue Li1,2, Wei-Feng Chen1,2, Zi-Ye Xu3, Zu-Qiang Liu1,2, Yun Wang1,2, Ji-Yuan Zhang1,2, Ya-Yun Gu4,5, Lu Yao1,2, Yan-Fang Tan1,2, Xiang-Jun Chen6, Bo Deng6, Ke-Hao Wang1,2, Jia-Qi Xu1,2, Meng-Jiang He1,2, Zi-Han Geng1,2, Ke-Yang Fan1,2, Zhao-Chao Zhang1,2, Li Wang1,2, An-Yi Xiang1,2
and 6 other authorsHai-Ting Pan1,2, Zhi-Bin Hu4,5, Yun-Li Xie7, Cheng Wang4,5, Ping-Hong Zhou1,2, Quan-Lin Li1,2
ORCID iDs: Xiang-Jun Chen, Zhi-Bin Hu, Yun-Li Xie, Cheng Wang, Ping-Hong Zhou, Quan-Lin Li
  1. Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University,Shanghai, China
  2. Shanghai Collaborative Innovation Center of Endoscopy, Shanghai, China
  3. Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University,Nanjing, Jiangsu China
  4. Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University,Nanjing, Jiangsu China
  5. State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University,Nanjing, Jiangsu China
  6. Department of Neurology, Huashan Hospital, Fudan University,12 Wulumuqi Zhong Road, Shanghai, China
  7. Institutes of Brain Science, Fudan University,Shanghai, China
Institutions: Fudan University (China); Nanjing Medical University (China)
Journal: Nature communications, volume 17, issue 1, article 6805
Dates: received 15 July 2025; accepted 6 May 2026; published online 25 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-73358-9 · PMID 42185265 · PMCID PMC13385689 · OpenAlex W7162302413
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), mouse (organism), cellular / molecular (subfield)
Methods: Smoothing, state filtering, decompositions
Keywords: Achalasia, Autoimmunity
MeSH: B-Lymphocytes*, Esophageal Achalasia*, Frameshift Mutation*, Animals, Autoantibodies, CRISPR-Cas Systems, Disease Models, Animal, Esophageal Sphincter, Lower, Female, Humans, Lymphocyte Activation, Male, Mice, Mice, Inbred C57BL (* major topic)
Topic: Gastroesophageal reflux and treatments (Gastroenterology, Medicine), according to OpenAlex
Funding: National Natural Science Foundation of China (National Science Foundation of China) (82570629, 82500618)
Citations: not cited yet (Europe PMC); 57 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

xiaoqingli789/achalasia

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 6a18be9ee5fcb16116f969397d4ab651a6c5f358, 5 September 2026
Languages: Python (1), Shell (1)
Size: 3 files, 2 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: BCFtools (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
3 files
At the source: github.com/xiaoqingli789/achalasia.git

Code availability statement

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Read it in the paper: doi.org/10.1038/s41467-026-73358-9.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 2 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41467-026-73358-9.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 26 authors, 2 keywords, 14 MeSH terms, 1 funder, 57 references.

Cite

This paper

Li, X.-Q., Li, X.-Y., Chen, W.-F., Xu, Z.-Y., Liu, Z.-Q., Wang, Y., Zhang, J.-Y., Gu, Y.-Y., Yao, L., Tan, Y.-F., Chen, X.-J., Deng, B., Wang, K.-H., Xu, J.-Q., He, M.-J., Geng, Z.-H., Fan, K.-Y., Zhang, Z.-C., Wang, L., . . . Li, Q.-L. (2026). A frameshift variant in FAM129C contributes to achalasia through B cell responses against the GABA&lt;sub&gt;A&lt;/sub&gt; receptor. Nature communications, 17(1), 6805. https://doi.org/10.1038/s41467-026-73358-9

BibTeX

@article{li2026frameshift,
author = {Li, Xiao-Qing and Li, Xin-Yue and Chen, Wei-Feng and Xu, Zi-Ye and Liu, Zu-Qiang and Wang, Yun and Zhang, Ji-Yuan and Gu, Ya-Yun and Yao, Lu and Tan, Yan-Fang and Chen, Xiang-Jun and Deng, Bo and Wang, Ke-Hao and Xu, Jia-Qi and He, Meng-Jiang and Geng, Zi-Han and Fan, Ke-Yang and Zhang, Zhao-Chao and Wang, Li and Xiang, An-Yi and Pan, Hai-Ting and Hu, Zhi-Bin and Xie, Yun-Li and Wang, Cheng and Zhou, Ping-Hong and Li, Quan-Lin},
title = {{A frameshift variant in FAM129C contributes to achalasia through B cell responses against the GABA\&lt;sub\&gt;A\&lt;/sub\&gt; receptor}},
journal = {Nature communications},
year = {2026},
month = may,
volume = {17},
number = {1},
pages = {6805},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-73358-9},
url = {https://doi.org/10.1038/s41467-026-73358-9},
pmid = {42185265},
pmcid = {PMC13385689}
}

RIS

TY - JOUR
AU - Li, Xiao-Qing
AU - Li, Xin-Yue
AU - Chen, Wei-Feng
AU - Xu, Zi-Ye
AU - Liu, Zu-Qiang
AU - Wang, Yun
AU - Zhang, Ji-Yuan
AU - Gu, Ya-Yun
AU - Yao, Lu
AU - Tan, Yan-Fang
AU - Chen, Xiang-Jun
AU - Deng, Bo
AU - Wang, Ke-Hao
AU - Xu, Jia-Qi
AU - He, Meng-Jiang
AU - Geng, Zi-Han
AU - Fan, Ke-Yang
AU - Zhang, Zhao-Chao
AU - Wang, Li
AU - Xiang, An-Yi
AU - Pan, Hai-Ting
AU - Hu, Zhi-Bin
AU - Xie, Yun-Li
AU - Wang, Cheng
AU - Zhou, Ping-Hong
AU - Li, Quan-Lin
TI - A frameshift variant in FAM129C contributes to achalasia through B cell responses against the GABA&lt;sub&gt;A&lt;/sub&gt; receptor
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/05/25
VL - 17
IS - 1
SP - 6805
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-73358-9
UR - https://doi.org/10.1038/s41467-026-73358-9
LA - en
ER -

CSL-JSON

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"id": "10.1038/s41467-026-73358-9",
"type": "article-journal",
"title": "A frameshift variant in FAM129C contributes to achalasia through B cell responses against the GABA&lt;sub&gt;A&lt;/sub&gt; receptor",
"container-title": "Nature communications",
"author": [
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"family": "Li",
"given": "Xiao-Qing"
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{
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"given": "Zi-Ye"
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{
"family": "Liu",
"given": "Zu-Qiang"
},
{
"family": "Wang",
"given": "Yun"
},
{
"family": "Zhang",
"given": "Ji-Yuan"
},
{
"family": "Gu",
"given": "Ya-Yun"
},
{
"family": "Yao",
"given": "Lu"
},
{
"family": "Tan",
"given": "Yan-Fang"
},
{
"family": "Chen",
"given": "Xiang-Jun"
},
{
"family": "Deng",
"given": "Bo"
},
{
"family": "Wang",
"given": "Ke-Hao"
},
{
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"given": "Jia-Qi"
},
{
"family": "He",
"given": "Meng-Jiang"
},
{
"family": "Geng",
"given": "Zi-Han"
},
{
"family": "Fan",
"given": "Ke-Yang"
},
{
"family": "Zhang",
"given": "Zhao-Chao"
},
{
"family": "Wang",
"given": "Li"
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{
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{
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"volume": "17",
"issue": "1",
"page": "6805",
"DOI": "10.1038/s41467-026-73358-9",
"PMID": "42185265",
"PMCID": "PMC13385689",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
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"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
25
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]
}
}

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