Using an original integrated proteomics and genetics strategy, we identified PLXNA4 as a new 58 susceptibility gene for PE whose exact role now needs to be further elucidated. Together with deep  64 vein thrombosis, pulmonary embolism forms the so-called venous thromboembolism, the 65 third most common cardiovascular disease, and its prevalence strongly increases with age. 66
While pulmonary embolism is observed in ~40% of patients with deep vein thrombosis, there 67
is currenly limited biomarkers that can help predicting which patients with deep vein 68 thrombosis are at risk of pulmonary embolism. We here deployed an Artificial Intelligence 69 based methodology integrating both plasma proteomics and genetics data to identify novel 70 biomarkers for PE. We thus identified the PLXNA4 gene as a novel molecular player involved 71
in the pathophysiology of pulmonary embolism. In particular, using two independent cohorts 72 totalling 1,881 patients with venous thromboembolism among which 467 experienced 73 pulmonary embolism, we identified a genetic polymorphism in the PLXNA4 gene that 74 associates with ~2 fold increased risk of pulmonary embolism in patients aged more than m  a  i  s  a  n  i  d  e  a  l  p  o  t  e  n  t  i  a  l  s  o  u  r  c  e  f  o  r  V  T  E  b  i  o  m  a  r  k  e  r  s  ;  t  h  e  i  n  t  r  a  v  a  s  c  u  l  a  r   99   c  o  m  p  a  r  t  m  e  n  t  i  t  s  e  l  f  i  s  t  h  e  s  i  t  e  o  f  d  i  s  e  a  s  e  m  a  n  i  f  e  s  t  a  t  i  o  n  a  n  d  t  e  s  t  s  a  r  e  r  e  l  a  t  i  v  e  l  y  n  o  n  -100   i  n  v  a  s  i  v  e  ,  q  u  i  c  k  a  n  d  c  h  e  a  p  .  S  e  v  e  r  a  l  t  y  p  e  s  o  f  m  o  l  e  c  u  l  a  r  d  e  t  e  r  m  i  n  a  n  t  s  c  a  n  b  e  a  s  s  e  s  s  e  d  i  n   101   p  l  a  s  m  a  s  a  m  p  l  e  s  i  n  c  l  u  d  i  n  g  m  i  c  r  o  R  N  A  s  ,  m  e  t  a  b  o  l  i  t  e  s  a  n  d  p  r  o  t  e  i  n  s  ,  a  n  d  a  l  l  o  f  t  h  e  m  h  a  v 109   r  i  s  k  ,  r  i  s  k  b  e  i  n  g  c  l  a  s  s  i  f  i  e  d  b  a  s  e  d  o  n  c  l  i  n  i  c  a  l  p  r  e  s  e  n  t  a  t  i  o  n  s  a  n  d  s  y  m  p  t  o  m  s  ,  w  i  t  h  p  l  a  s  m  a   110   s  a  m  p  l  e  s  p  r  o  f  i  l  e  d  b  y  m  a  t  r  i  x  -a  s  s  i  s  t  e  d  l  a  s  e  r  d  e  s  o  r  p  t  i  o  n  /  i  o  n  i  z  a  t  i  o  n  -t  i  m  e  -o  f  -f  l  i  g  h  t  /  t  i  m  e  -o  f  -111   f  l  i  g  h  t  m  a  s  s  s  p  e  c  t  r  o  m  e  t  r  y  (  M  A  L  D  I  -T  O  F  /  T  O  F  M  S ) .
. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted October 6, 2020. . https://doi.org/10.1101/2020.10.05.20207001 doi: medRxiv preprint  I  n  t  h  i  s  w  o  r  k  ,  w  e  a  i  m  a  t  i  d  e  n  t  i  f  y  i  n  g  n  o  v  e  l  m  o  l  e  c  u  l  a  r  p  h  e  n  o  t  y  p  e  s  t  h  a  t  c  o  u  l  d  h  e  l  p  i  n   113   b  e  t  t  e  r  c  h  a  r  a  c  t  e  r  i  z  i  n  g  t  h  e  b  i  o  l  o  g  i  c  a  l  m  e  c  h  a  n  i  s  m  s  i  n  v  o  l  v  e  d  i  n  t  h  e  d  e  v  e  l  o  p  m  e  n  t  o  f  P  E  i  n   114   V  T  E  p  a  t  i  e  n  t  s  .  F  o  r  t  h  i  s  ,  2  3  4  p  l  a  s  m  a  p  r  o  t  e  i  n  s  t  a  r  g  e  t  e  d  w  i  t  h  3  7  6  p  r  o  t  e  i  n  s  p  e  c  i  f  i  c   115   a  n  t  i  b  o  d  i  e  s  ,  w  i  t  h  t  h  e  m  a  j  o  r  p  a  r  t  d  e  r  i  v  e  d  f  r  o  m  t  h  e  H  u  m  a  n  P  r  o  t  e  i  n  A  t  l  a  s  (  H  P  A  )  r  e  p  o  s  i  t  o  r  y   116   [  1  3  ]  w  e  r  e  p  r  o  f  i  l  e  d  i  n  1  3  8  8  V  T  E  p  a  t  i  e  n  t  s  s  e  l  e  c  t  e  d  f  r  o  m  t  h  e  M  A  R  T  H  A  s  t  u  d  y  [  1  4  ,  1  5  ]  a  n  d   117   f  r  o  m  w  h  o  m  2  8  3  h  a  d  e  x  p  e  r  i  e  n  c  e  d  a  s  y  m  p  t  o  m  a  t  i  c  P  E  e  v  e  n  t  .  T  o  e  x  p  l  o  r  e  f  a  r  b  e  y  o  n  d  t  h  e   118   s  e  a  r  c  h  f  o  r  l  i  n  e  a  r  a  s  s  o  c  i  a  t  i  o  n  s  b  e  t  w  e  e  n  p  r  o  t  e  i  n  l  e  v  e  l  s  a  n  d  P  E  r  i  s  k  a  n  d  t  o  i  d  e  n  t  i  f  y  m  o  r r  i  s  k  w  h  i  c  h  w  o  u  l  d  ,  i  n  a  d  d  i  t  i  o  n  ,  h  a  v  e  a  m  o  r  e  m  e  a  n  i  n  g  f  u  l  b  i  o  l  o  g  i  c  a  l  i  n  t  e  r  p  r  e  t  a  t  i  o  n  .  A  s   131   M  A  R  T  H  A  p  a  t  i  e  n  t  s  h  a  v  e  b  e  e  n  p  r  e  v  i  o  u  s  l  y  t  y  p  e  d  f  o  r  g  e  n  o  m  e  -w  i  d  e  g  e  n  o  t  y  p  e  d  a  t  a  ,  w  e  t  h  e  n   132   c  o  n  d  u  c  t  e  d  a  g  e  n  o  m  e  w  i  d  e  a  s  s  o  c  i  a  t  i  o  n  s  t  u  d  y  o  f  t  h  e  L  I  M  E  p  r  e  d  i  c  t  o  r  o  f  P  E  i  n  o  r  d  e  r  t  o   133   d  e  t  e  c  t  s  i  n  g  l  e  n  u  c  l  e  o  t  i  d  e  p  o  l  y  m  o  r  p  h  i  s  m  s  (  S  N  P  s  )  a  s  s  o  c  i  a  t  e  d  w  i  t  h  t  h  e  p  r  e  d  i  c  t  o  r  w  i  t  h  t  h  e   134   h  o  p  e  t  h  a  t  t  h  e  i  n  t  e  g  r  a  t  i  o  n  o  f  g  e  n  e  t  i  c  a  n  d  p  r  o  t  e  o  m  i  c  d  a  t  a  c  o  u  l  d  p  r  o  v  i  d  e  a  d  d  i  t  i  o  n  a  l  i  n  s  i  g  h  t . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
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170 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
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193 
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The copyright holder for this preprint this version posted October 6, 2020. . https://doi.org/10.1101/2020.10.05.20207001 doi: medRxiv preprint e  t  o  p  a  t  i  e  n  t  s  e  l  e  c  t  i  o  n  c  r  i  t  e  r  i  a  (  i  .  e  a  c  c  o  r  d  i  n  g  t  o  a  g  e  .  )  W  e  t  h  u  s  s  p  l  i  t  t  h  e  E  O  V  T   253   s  a  m  p  l  e  s  a  c  c  o  r  d  i  n  g  t  o  t  h  e  m  e  d  i  a  n  o  f  a  g  e  o  f  V  T  E  o  n  s  e  t  ,  t  h  a  t  w  a  s  3  7  y  r  s  .  A  s  s  h  o  w  n  i  n  T  a  b  l  e   254   4  ,  t  h  e  p  a  t  t  e  r  n  o  f  a  s  s  o  c  i  a  t  i  o  n  o  f  r  s  1  4  2  4  5  9  7  w  i  t  h  P  E  s  l  i  g  h  t  l  y  d  i  f  f  e  r  e  d  a  c  c  o  r  d  i  n  g  t  o  a  g 
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The copyright holder for this preprint this version posted October 6, 2020. 
. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint this version posted October 6, 2020. 
. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint this version posted October 6, 2020. . https://doi.org/10.1101/2020.10.05.20207001 doi: medRxiv preprint a n t  i  b  o  d  y  t  a  r  g  e  t  i  n  g  P  L  X  N  A  4  w  a  s  a  v  a  i  l  a  b  l  e  w  h  e  n  t  h  e  s  c  r  e  e  n  i  n  g  p  h  a  s  e  o  f  t  h  i  s  w  o  r  k  w  a  s   380   i  n  i  t  i  a  t  e  d  p  r  e  v  e  n  t  i  n  g  u  s  f  r  o  m  v  a  l  i  d  a  t  i  n  g  f  u  r  t  h  e  r  i  t  s  a  s  s  o  c  i  a  t  i  o  n  w  i  t  h  P  E  .  S  e  c  o  n  d  ,  n  o   381   p  r  o  t  e  o  m  i  c  d  a  t  a  w  a  s  a  v  a  i  l  a  b  l  e  i  n  t  h  e  E  O  V  T  s  t  u  d  y  t  o  f  o  r  m  a  l  l  y  r  e  p  l  i  c  a  t  e  t  h  e  a  s  s  o  c  i  a  t  i  o  n  o 
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The copyright holder for this preprint this version posted October 6, 2020. . 1  4   o  f  a  n  y  w  e  l  l  c  h  a  r  a  c  t  e  r  i  z  e  d  g  e  n  e  t  i  c  r  i  s  k  f  a  c  t  o  r  s  i  n  c  l  u  d  i  n  g  a  n  t  i  t  h  r  o  m  b  i  n  ,  p  r  o  t  e  i  n  C  o  r   413   p  r  o  t  e  i  n  S  d  e  f  i  c  i  e  n  c  y  ,  h  o  m  o  z  y  g  o  s  i  t  y  f  o  r  F  V  L  e  i  d  e  n  o  r  F  a  c  t  o  r  I  I  2  0  2  1  0  A  ,  a  n  d  l  u  p  u  s   414   a  n  t  i  c  o  a  g  u  l  a  n  t  .  D  e  t  a  i  l  e  d  d  e  s  c  r  i  p  t  i  o  n  o  f  t  h  e  M  A  R  T  H  A  p  o  p  u  l  a  t  i  o  n  h  a  s  b  e  e  n  p  r  o  v  i  d  e 
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The copyright holder for this preprint this version posted October 6, 2020. c  o  m  p  l  e  x  e  s  w  e  r  e  c  r  o  s  s  -l  i  n  k  e  d  b  y  r  e  s  u  s  p  e  n  d  i  n  g  t  h  e  b  e  a  d  s  i  n  0  .  4  %  P  F  A  -P  B  S  f  o  r  1  0  m  i  n  .  R  -446   p  h  y  c  o  e  r  y  t  h  r  i  n  -c  o  n  j  u  g  a  t  e  d  s  t  r  e  p  t  a  v  i  d  i  n  (  1  :  7  5  0  ,  P  B  S  -T  ;  I  n  v  i  t  r  o  g  e  n  )  w  a  s  a  d  d  e  d  t  o  a  l  l   447   s  a  m  p  l  e  s  f  o  r  3  0  m  i  n  f  o  l  l  o  w  e  d  b  y  2  t  i  m  e  s  w  a  s  h  e  s  .  R  e  l  a  t  i  v  e  a  m  o  u  n  t  o  f  e  a  c  h  p  r  o  t  e  i 
. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint this version posted October 6, 2020. . 
. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint this version posted October 6, 2020. w  a  s  t  h  e  n  b  a  c  k  p  r  o  p  a  g  a  t  e  d  u  s  i  n  g  a  g  r  a  d  i  e  n  t  d  e  s  c  e  n  t  a  l  g  o  r  i  t  h  m  [  5  2  ]  (  w  i  t  h  l  e  a  r  n  i  n  g  o  f  0  .  0  1   512   a  n  d  b  a  t  c  h  s  i  z  e  o  f  3  2  )  t  o  u  p  d  a  t  e  w  e  i  g  h  t  s  a  c  c  o  r  d  i  n  g  t  o  t  h  e  i  r  c  o  n  t  r  i  b  u  t  i  o  n  t  o  t  h  e  e  r  r  o  r  .  I  n   513   o  r  d  e  r  t  o  r  e  d  u  c  e  o  v  e  r  -f  i  t  t  i  n  g  a  n  d  o  b  t  a  i  n  t  h  e  b  e  s  t  p  e  r  f  o  r  m  i  n  g  m  o  d  e  l  ,  t  h  e  c  a  l  l  b  a  c  k  f  e  a  t  u  r 
. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted October 6, 2020. . https://doi.org/10.1101/2020.10.05.20207001 doi: medRxiv preprint  m  o  d  e  l  b  a  s  e  d  o  n  t  h  e  i  n  v  e  r  s  e  -v  a  r  i  a  n  c  e  w  e  i  g  h  t  i  n  g  a  n  d  h  e  t  e  r  o  g  e  n  e  i  t  y  o  f  a  s  s  o  c  i  a  t  i  o  n   545   b  e  t  w  e  e  n  t  h  e  t  w  o  s  t  u  d  i  e  s  w  a  s  a  s  s  e  s  s  e  d  b  y  t  h  e  C  o  c  h  r  a  n  -M  a  n  t  e  l  -H  a  e  n  s  z  e  l  t  e  s  t  s  t  a  t  i  s  t  i  c  s  n  -546   M  a  n  t  e  l  -H  a  e  n  s  z  e  l  t  e  s  t  s  t  a  t  i  s  t  i  c  [  5 . Variant calling was 567 performed using the GATK HaplotypeCaller (GenomeAnalysisTK-v3.3-0, 568 https://software.broadinstitute.org/gatk/documentation/article.php?id=4148). Single-sample 569 gVCFs files were then aggregated using GATK CombineGVCFs and joint genotyping calling 570 performed by GATK GenotypeGVCFs. Recalibration was then conducted on the whole gVCF 571 following GATK guidelines. Following GATK VQSR, we retained single nucleotide variants 572 in the 99.5% tranche sensitivity threshold and indels in the 99% tranche sensitivity threshold 573 for further analysis and annotated them using Annovar [55] . 574
As a strategy to identify candidate variants that could explain the VTE phenotype in 575 individuals with discordant class prediction, we first prioritized variants that were likely 576 functional (stop loss/stop gain, frameshift, non-synonymous and splicing variants), located in 577 known VTE associated genes (ABO, ARID4A, C4BPB, EIF5A, F2, F3, F5, F8, F9, F13A1, 578 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted October 6, 2020. FGG, GRK5, MPHOSPH9, MAST2, NUGCC, OSMR, PLAT, PLCG2, PLEK1, PROC,  579   PROS1, SCARA5, SERPINC1, SLC44A2, STAB2, STX10, STXBP5, THBD, TSPAN15,  580 VWF) [56-58], that have not been reported or at a low frequency (<1‰) in public genomic 581 data repositories (dbSNP, GnomAD) and that was present in only one of the 200 sequenced 582 patients. If no candidate variants was identified in known VTE genes, we extended our search 583 to whole coding genes and also took into account the predicted deleteriousness of selected 584 candidates using in silico tools such as SIFT, PolyPhen and CADD-v1. 
. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)
The copyright holder for this preprint this version posted October 6, 2020. 