diff --git a/grobid-trainer/resources/dataset/segmentation/corpus/raw/pub.1160333290.training.segmentation b/grobid-trainer/resources/dataset/segmentation/corpus/raw/pub.1160333290.training.segmentation
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+Table 1. table T Ta Tab Tabl BLOCKSTART PAGEIN NEWFONT LOWERFONT 1 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 3 0 .. 2 10 0 1 0 0 1
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+Glomerular basement glomerular G Gl Glo Glom BLOCKSTART PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 0 0 0 0 0 0 3 0 no 0 9 0 0 0 0 1
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+AD AD ad A AD AD AD BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 no 0 0 0 0 0 0 1
+Sodium voltage-gated sodium S So Sod Sodi BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 - 1 8 0 0 0 0 1
+SCN11A SCN11A scn11a S SC SCN SCN1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 no 0 1 0 0 0 0 1
+chr3 chr3 chr3 c ch chr chr3 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 no 0 0 0 0 0 0 1
+AD AD ad A AD AD AD BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 no 0 0 0 0 0 0 1
+Sodium voltage-gated sodium S So Sod Sodi BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 - 1 8 0 0 0 0 1
+SCN1,3,8A SCN1,3,8A scn1,3,8a S SC SCN SCN1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 ,, 2 1 0 0 0 0 1
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+AD/AD/AD AD/AD/AD ad/ad/ad A AD AD/ AD/A BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 5 // 2 1 0 0 0 0 1
+Sodium channel sodium S So Sod Sodi BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 // 2 6 0 0 0 0 1
+SCN9A SCN9A scn9a S SC SCN SCN9 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 no 0 1 0 0 0 0 1
+chr2 chr2 chr2 c ch chr chr2 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 no 0 0 0 0 0 0 1
+AR, AD ar, A AR AR, AR, BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 5 , 1 1 0 0 0 0 1
+Sodium voltage-gated sodium S So Sod Sodi BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 - 1 8 0 0 0 0 1
+KCNQ KCNQ kcnq K KC KCN KCNQ BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 5 no 0 0 0 0 0 0 1
+chr11 chr11 chr11 c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 no 0 1 0 0 0 0 1
+AR, AD ar, A AR AR, AR, BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 5 , 1 1 0 0 0 0 1
+Potassium voltage-gated potassium P Po Pot Pota BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 - 1 8 0 0 0 0 1
+Pain synaptic pain P Pa Pai Pain BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 no 0 5 0 0 0 0 1
+NR1, 2 nr1, N NR NR1 NR1, BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 , 1 1 0 0 0 0 1
+chr9/ chr9/ chr9/ c ch chr chr9 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 / 1 1 0 0 0 0 1
+AR, AD ar, A AR AR, AR, BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 5 , 1 1 0 0 0 0 1
+Nuclear receptor nuclear N Nu Nuc Nucl BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 5 / 1 5 0 0 0 0 1
+GRIA1-4 GRIA1-4 gria1-4 G GR GRI GRIA BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 - 1 1 0 0 0 0 1
+chr5/chr4/chrX/chr11 chr5/chr4/chrX/chr11 chr5/chr4/chrx/chr11 c ch chr chr5 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 /// 3 3 0 0 0 0 1
+AR, AD/ ar, A AR AR, AR, BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 5 ,/// 4 3 0 0 0 0 1
+AMPA receptor ampa A AM AMP AMPA BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 5 - 1 3 0 0 0 0 1
+NK1R NK1R nk1r N NK NK1 NK1R BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 no 0 0 0 0 0 0 1
+chr2 chr2 chr2 c ch chr chr2 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 no 0 0 0 0 0 0 1
+Tachykinin receptor tachykinin T Ta Tac Tach BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 5 no 0 4 0 0 0 0 1
+CACNA1A-I, S cacna1a-i, C CA CAC CACN BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 -, 2 2 0 0 0 0 1
+chr19/chr9/chr12/chr3/ chr19/chr9/chr12/chr3/ chr19/chr9/chr12/chr3/ c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 //// 4 4 0 0 0 0 1
+chr1/chrX/chr17/chr16/ chr1/chrX/chr17/chr16/ chr1/chrx/chr17/chr16/ c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 //// 4 4 0 0 0 0 1
+chr22/chr1 chr22/chr1 chr22/chr1 c ch chr chr2 BLOCKEND PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 5 / 1 2 0 0 0 0 1
+AD/ AR/ ad/ A AD AD/ AD/ BLOCKSTART PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 10 ///,// 6 10 0 1 0 0 1
+XL, XLR/ xl, X XL XL, XL, BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 10 ,//// 5 9 0 1 0 0 1
+R, AD r, R R, R, R, BLOCKEND PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 10 , 1 2 0 1 0 0 1
+Calcium voltage-gated calcium C Ca Cal Calc BLOCKSTART PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 11 -- 2 10 0 1 0 0 1
+CACNA2D1 CACNA2D1 cacna2d1 C CA CAC CACN BLOCKSTART PAGEIN NEWFONT SAMEFONTSIZE 0 1 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 11 no 0 1 0 1 0 0 1
+chr7 chr7 chr7 c ch chr chr7 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 11 no 0 0 0 1 0 0 1
+AR AR ar A AR AR AR BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 11 no 0 0 0 1 0 0 1
+Calcium voltage-gated calcium C Ca Cal Calc BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 11 - 1 10 0 1 0 0 1
+delta 1 delta d de del delt BLOCKEND PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS NODIGIT 0 1 1 0 0 0 0 0 4 11 no 0 1 0 1 0 0 1
+(continued) (continued) (continued) ( (c (co (con BLOCKSTART PAGEEND SAMEFONT SAMEFONTSIZE 0 1 NOCAPS NODIGIT 0 0 0 0 0 0 0 0 4 11 () 2 10 0 1 0 0 1
+Sharma et sharma S Sh Sha Shar BLOCKSTART PAGESTART SAMEFONT HIGHERFONT 0 1 INITCAP NODIGIT 0 1 0 0 0 0 0 0 4 0 no 0 10 0 1 1 0 0
+5 5 5 5 5 5 5 BLOCKSTART PAGEIN NEWFONT SAMEFONTSIZE 0 0 NOCAPS ALLDIGIT 1 0 0 0 0 0 0 0 4 0 no 0 10 0 1 0 0 0
+Gene name gene G Ge Gen Gene BLOCKSTART PAGEIN SAMEFONT LOWERFONT 0 0 INITCAP NODIGIT 0 1 0 0 0 0 0 0 4 0 no 0 5 0 1 0 0 1
+Chromosome number chromosome C Ch Chr Chro BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 0 no 0 10 0 1 0 0 1
+Inheritance a inheritance I In Inh Inhe BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 0 no 0 7 0 1 0 0 1
+Gene annotation gene G Ge Gen Gene BLOCKEND PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 1 0 0 0 0 0 0 4 0 no 0 8 0 1 0 0 1
+Pain modulation pain P Pa Pai Pain BLOCKSTART PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 0 no 0 4 0 0 0 0 1
+BDNF BDNF bdnf B BD BDN BDNF BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 0 no 0 1 0 0 0 0 1
+chr11 chr11 chr11 c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 0 no 0 1 0 0 0 0 1
+Brain-derived neurotrophic brain-derived B Br Bra Brai BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 0 - 1 9 0 0 0 0 1
+OPRD1/M1/K1 OPRD1/M1/K1 oprd1/m1/k1 O OP OPR OPRD BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 0 // 2 3 0 0 0 0 1
+chr1/ chr6/ chr1/ c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 0 // 2 4 0 0 0 0 1
+Opioid receptor opioid O Op Opi Opio BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 0 // 2 10 0 0 0 0 1
+CNR1 CNR1 cnr1 C CN CNR CNR1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 0 no 0 1 0 0 0 0 1
+chr6 chr6 chr6 c ch chr chr6 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 0 no 0 1 0 0 0 0 1
+Cannabinoid receptor cannabinoid C Ca Can Cann BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 0 no 0 6 0 0 0 0 1
+GABRs (GABRD/E/ gabrs G GA GAB GABR BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 0 (// 3 4 0 0 0 0 1
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+chr4/chrX/chr4/chr15/ chr4/chrX/chr4/chr15/ chr4/chrx/chr4/chr15/ c ch chr chr4 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 1 //// 4 8 0 0 0 0 1
+chr5/chr4/chr5/chr15/ chr5/chr4/chr5/chr15/ chr5/chr4/chr5/chr15/ c ch chr chr5 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 1 //// 4 8 0 0 0 0 1
+chr4/chr5/chr15/chr6/ chr4/chr5/chr15/chr6/ chr4/chr5/chr15/chr6/ c ch chr chr4 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 1 //// 4 8 0 0 0 0 1
+chr6/chr3 chr6/chr3 chr6/chr3 c ch chr chr6 BLOCKEND PAGEIN SAMEFONT SAMEFONTSIZE 0 0 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 1 / 1 3 0 0 0 0 1
+AD/ M/ ad/ A AD AD/ AD/ BLOCKSTART PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 1 /////,/ 7 10 0 0 0 0 1
+XL/ M/ xl/ X XL XL/ XL/ BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 1 ////// 6 8 0 0 0 0 1
+AD/ M/ ad/ A AD AD/ AD/ BLOCKEND PAGEIN SAMEFONT SAMEFONTSIZE 0 0 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 1 ////// 6 8 0 0 0 0 1
+Gamma-aminobutyric acid gamma-aminobutyric G Ga Gam Gamm BLOCKSTART PAGEIN SAMEFONT SAMEFONTSIZE 0 0 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 - 1 10 0 0 0 0 1
+TNF TNF tnf T TN TNF TNF BLOCKSTART PAGEIN NEWFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 0 0 0 0 0 1
+chr6 chr6 chr6 c ch chr chr6 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+AD AD ad A AD AD AD BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 1 0 0 0 0 0 4 2 no 0 0 0 0 0 0 1
+Tumor necrosis tumor T Tu Tum Tumo BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 2 no 0 4 0 0 0 0 1
+PLA2G2A PLA2G2A pla2g2a P PL PLA PLA2 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
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+AD, SMu ad, A AD AD, AD, BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 1 0 0 0 0 0 4 2 , 1 1 0 0 0 0 1
+Phospholipase A2 phospholipase P Ph Pho Phos BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 3 0 0 0 0 1
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+M/ Mu, m/ M M/ M/ M/ BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 /,,,///// 9 10 0 0 0 0 1
+COX2 COX2 cox2 C CO COX COX2 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+chrMT chrMT chrmt c ch chr chrM BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+Cytochrome C cytochrome C Cy Cyt Cyto BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 6 0 0 0 0 1
+NTRK1 NTRK1 ntrk1 N NT NTR NTRK BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+chr1 chr1 chr1 c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+AR AR ar A AR AR AR BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 0 0 0 0 0 1
+High affinity high H Hi Hig High BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 1 1 0 0 0 0 0 4 2 no 0 9 0 0 0 0 1
+NGF NGF ngf N NG NGF NGF BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 0 0 0 0 0 1
+chr1 chr1 chr1 c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+AR AR ar A AR AR AR BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 0 0 0 0 0 1
+Beta-nerve growth beta-nerve B Be Bet Beta BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 2 - 1 5 0 0 0 0 1
+GDNF GDNF gdnf G GD GDN GDNF BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+chr5 chr5 chr5 c ch chr chr5 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+AD AD ad A AD AD AD BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 1 0 0 0 0 0 4 2 no 0 0 0 0 0 0 1
+Glial cell glial G Gl Gli Glia BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 - 1 9 0 0 0 0 1
+LIF LIF lif L LI LIF LIF BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 0 0 0 0 0 1
+chr22 chr22 chr22 c ch chr chr2 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+AD AD ad A AD AD AD BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 1 0 0 0 0 0 4 2 no 0 0 0 0 0 0 1
+Leukemia inhibitory leukemia L Le Leu Leuk BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 5 0 0 0 0 1
+CCL2 CCL2 ccl2 C CC CCL CCL2 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+chr17 chr17 chr17 c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+C-C motif c-c C C- C-C C-C BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 - 1 4 0 0 0 0 1
+CNR2 CNR2 cnr2 C CN CNR CNR2 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+chr1 chr1 chr1 c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 1 0 0 0 0 1
+Cannabinoid receptor cannabinoid C Ca Can Cann BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 0 0 0 0 0 0 4 2 no 0 4 0 0 0 0 1
+TLR2/4 TLR2/4 tlr2/4 T TL TLR TLR2 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 / 1 1 0 0 0 0 1
+chr4/chr9 chr4/chr9 chr4/chr9 c ch chr chr4 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 / 1 2 0 0 0 0 1
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+Toll-like receptor toll-like T To Tol Toll BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 1 0 0 0 0 0 4 2 -/ 2 4 0 0 0 0 1
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+chr12/chr12 chr12/chr12 chr12/chr12 c ch chr chr1 BLOCKIN PAGEIN SAMEFONT SAMEFONTSIZE 0 1 NOCAPS CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 / 1 2 0 0 0 0 1
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+CX3C chemokine cx3c C CX CX3 CX3C BLOCKEND PAGEIN SAMEFONT SAMEFONTSIZE 0 1 ALLCAP CONTAINSDIGITS 0 0 0 0 0 0 0 0 4 2 no 0 5 0 0 0 0 1
+a a a a a a a BLOCKSTART PAGEIN NEWFONT LOWERFONT 0 0 NOCAPS NODIGIT 1 0 1 0 0 0 0 0 5 4 no 0 10 0 1 0 0 1
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+been approved been b be bee been BLOCKSTART PAGEIN NEWFONT HIGHERFONT 0 0 NOCAPS NODIGIT 0 0 1 0 0 0 0 0 5 5 no 0 10 0 1 0 0 1
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+Design Design design D De Des Desi BLOCKSTART PAGEIN NEWFONT HIGHERFONT 1 0 INITCAP NODIGIT 0 0 1 0 0 0 0 0 5 5 no 0 10 0 1 0 0 1
+Number of number N Nu Num Numb BLOCKSTART PAGEIN NEWFONT SAMEFONTSIZE 0 1 INITCAP NODIGIT 0 0 1 0 0 0 0 0 5 5 no 0 10 0 0 0 0 1
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+			<front>Creative Commons Non Commercial CC BY-NC: This article is distributed under the terms of the Creative Commons Attribution-<lb/>NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and <lb/>distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages <lb/>(https://us.sagepub.com/en-us/nam/open-access-at-sage). <lb/>Journal canadien de la santé et de la maladie rénale <lb/>https://doi.org/10.1177/20543581231183856 <lb/>Canadian Journal of Kidney Health <lb/>and Disease <lb/>Volume 10: 1 -10 <lb/>© The Author(s) 2023 <lb/>Article reuse guidelines: <lb/>sagepub.com/journals-permissions <lb/>DOI: 10.1177/20543581231183856 <lb/>journals.sagepub.com/home/cjk <lb/>Basic Research Protocol <lb/>1183856C JKXXX10.1177/20543581231183856Canadian Journal of Kidney Health and DiseaseSharma et al <lb/>research-article20232023 <lb/>Basic Research Protocol: Exome <lb/>Sequencing in Adults With Loin Pain <lb/>Hematuria Syndrome: A Pilot Study <lb/>Aditi Sharma 1 , Matthew B. Lanktree 2,3 , Sarah Liskowich 4 , <lb/>Pouneh Dokouhaki 5 , and Bhanu Prasad 6,7 <lb/>Abstract <lb/>Background: Loin pain hematuria syndrome (LPHS) is a poorly understood clinical syndrome characterized by hematuria and <lb/>either unilateral or bilateral severe kidney pain in the absence of identifiable urological disease. Loin pain hematuria syndrome <lb/>imposes a significant health and economic impact with a loss of productivity and quality of life in a young population. Owing <lb/>to an incomplete understanding of its pathophysiology, treatment has been limited to nonspecific pain management. Nearly <lb/>60 years after its initial description, we are no further ahead in understanding the molecular pathways involved in LPHS. <lb/>Objective: To outline the study design for exome sequencing in adults with LPHS and their families. <lb/>Methods: In this single-center case series, 24 patients with LPHS and 2 additional first-degree family members per participant <lb/>will be recruited. DNA extracted from venous blood samples will undergo exome sequencing on the Illumina NovaSeq <lb/>6000 System at 100× depth and will be assessed for pathogenic variants in genes associated with hematuria (number of <lb/>genes in: glomerular endothelium [n = 10] and basement membrane [n = 8]), and pain pathways (number of genes in: pain <lb/>transduction [n = 17], conduction [n = 8], synaptic transmission [n = 37], and modulation [n = 27]). We will further <lb/>examine identified potentially pathogenic variants that co-segregate with LPHS features among affected families. <lb/>Conclusions: This pilot study may identify new directions for an investigation into the molecular mechanisms underlying <lb/>LPHS. <lb/>Abrégé <lb/>Contexte: Le syndrome de lombalgie-hématurie est un syndrome clinique encore mal compris qui se caractérise par une <lb/>hématurie et une forte douleur rénale unilatérale ou bilatérale en l&apos;absence d&apos;une maladie urologique identifiable. Le syndrome <lb/>de lombalgie-hématurie a une incidence importante sur la santé et l&apos;économie en entraînant une perte de productivité et <lb/>de qualité de vie dans une population jeune. La compréhension de la physiopathologie de ce syndrome étant incomplète, le <lb/>traitement a été limité à la gestion non spécifique de la douleur. Près de soixante ans après sa description initiale, nous en <lb/>sommes au même point dans la compréhension des voies moléculaires impliquées dans le syndrome de lombalgie-hématurie. <lb/>Objectif: Décrire le plan de l&apos;étude pour le séquençage de l&apos;exome chez les adultes atteints du syndrome de lombalgie-<lb/>hématurie et des membres de leur famille. <lb/>Méthodologie: Pour cette série de cas menée dans un seul center, nous recruterons 24 patients atteints du syndrome de <lb/>lombalgie-hématurie et deux membres au premier degré de leur famille. L&apos;ADN extrait d&apos;échantillons de sang veineux sera <lb/>soumis à un séquençage de l&apos;exome sur le système Ilumina NovaSeq 6000 réglé à 100X de profondeur. Il sera également <lb/>analysé pour la présence de variants pathogènes dans les gènes associés à l&apos;hématurie (nombre de gènes dans l&apos;endothélium <lb/>glomérulaire [n = 10] et la membrane basale [n = 8]), et aux voies de transmission de la douleur (nombre de gènes dans la <lb/>transduction [n = 17], la conduction [n = 8], la transmission synaptique [n = 37] et la modulation [n = 27] de la douleur). <lb/>Nous poursuivrons l&apos;examen des variants potentiellement pathogènes identifiés qui co-ségrègent avec les caractéristiques du <lb/>syndrome de lombalgie-hématurie parmi les familles touchées. <lb/>Conclusion: Cette étude pilote pourrait révéler de nouveaux axes de recherche sur les mécanismes moléculaires qui sous-<lb/>tendent le syndrome de lombalgie-hématurie. <lb/>Keywords <lb/>loin pain hematuria syndrome, exome sequencing, rare disease, eGFR, hematuria, chronic pain <lb/>Received November 9, 2022. Accepted for publication May 18, 2023. <lb/></front>
+
+			<page>2 <lb/></page>
+
+			<note place="headnote">Canadian Journal of Kidney Health and Disease <lb/></note>
+
+			<body>What was known before <lb/>Hematuria in patients with loin pain hematuria syndrome is <lb/>glomerular in origin, but the source of pain is a mystery. <lb/>What this adds <lb/>We outline our study protocol to investigate genetic variants <lb/>in the glomerular endothelium and basement membrane as <lb/>potential contributors to glomerular hematuria in LPHS. We <lb/>will also evaluate variants in candidate genes in pain path-<lb/>ways. We anticipate that the results from this study will iden-<lb/>tify new directions for an investigation into the molecular <lb/>mechanisms underlying LPHS pathophysiology. <lb/>Introduction <lb/>Loin pain hematuria syndrome (LPHS) remains a poorly <lb/>understood chronic pain disorder since its first description in <lb/>1967. 1 With a reported prevalence of .012%, 2 it typically <lb/>affects young women in their late 20s or early 30s. Patients <lb/>with LPHS experience debilitating flank (loin) pain, which <lb/>can be unilateral or bilateral, along with gross or microscopic <lb/>hematuria. 2,3 In 1996, Hebert et al proposed glomerular <lb/>hematuria as the instigating event, sequentially leading to <lb/>tubular obstruction, back leak of glomerular filtrate, and <lb/>local parenchymal edema promoting compression of adja-<lb/>cent tubules and subsequent capsular stretch leading to pain. 4 <lb/>However, the absence of pain in other clinical conditions that <lb/>include red blood cell and cellular cast formation including <lb/>acute tubular necrosis (ATN), pyelonephritis, IgA nephropa-<lb/>thy (Henoch Schoenlein Syndrome), vasculitis, and antiglo-<lb/>merular basement membrane disease argues against the <lb/>validity of this mechanism. We believe LPHS likely repre-<lb/>sents a heterogeneous collection of cases that present with <lb/>shared phenotypic features of glomerular hematuria and pain <lb/>originating from the kidneys but with different pathogenesis <lb/>and natural history. <lb/>Glomerular hematuria in the absence of proteinuria is <lb/>typically associated with defects in the glomerular filtration <lb/>barrier, as most forms of podocyte injury lead to some degree <lb/>of proteinuria. The remaining structural components of the <lb/>filtration barrier include the glomerular basement membrane <lb/>(GBM) and the specialized fenestrated glomerular endothe-<lb/>lial cells (GEC). Glomerular basement membrane plays a <lb/>key role in keeping the cellular elements of blood from tres-<lb/>passing into the urinary space. The best technique to evaluate <lb/>GBM structure is electron microscopy of a kidney biopsy. <lb/>However, electron microscopy has not revealed structural <lb/>deficits in the GBM structure of most patient&apos;s with LPHS. 4 <lb/>There is a real need for an enhanced understanding of <lb/>LPHS pathogenesis using advanced cellular and molecular <lb/>technologies to explicate, detect, and diagnose both its pres-<lb/>ence and probable outcome to treatment. Rapid advances in <lb/>next-generation sequencing (NGS) technologies over the last <lb/>2 decades have enabled the extensive unbiased interrogation <lb/>of the exome, with patient/parent trio being a successful <lb/>approach for identifying candidates and de novo variants. <lb/>Specifically, the trio exome analysis has added crucial <lb/>insights for diseases with complex pathogenesis and a heter-<lb/>ogenous rate of progressions, such as IgA nephropathy, 5 ste-<lb/>roid-resistant nephrotic syndrome, 6 nephrolithiasis, and <lb/>nephrocalcinosis. 7 In addition, for diseases like chronic kid-<lb/>ney disease (CKD) of unknown cause, where renal ultra-<lb/>sounds and kidney biopsies are uninformative and are unable <lb/>to distinguish between multiple diseases, exome sequencing <lb/>has led to the identification of 500 monogenic causes of <lb/>CKD, 8,9 which in turn led to an increased diagnosis rate. 10 <lb/>Similarly, a phenotypic spectrum of GBM abnormalities has <lb/>been reported in patients with rare pathogenic variants in <lb/>type IV collagen genes (COL4A3/4/5), classically associated <lb/>with Alport syndrome, ranging from severe abnormalities in <lb/>GBM thickness to no visible abnormalities at all. The identi-<lb/>fication of more than 1000 mutations in the COL43/4/5 <lb/>genes 11,12 that encode for the type IV collagen A3A4A5 het-<lb/>erotrimer (a major component of the GBM), has led to the <lb/>reclassification of Alport syndrome and benign familial <lb/>hematuria/thin basement membrane nephropathy (TBMN) <lb/>as type IV collagen nephropathies, 13 promoting genetic test-<lb/>ing as the gold standard in understanding the prognosis of the <lb/>phenotype. Therefore, we believe that the next logical step <lb/>will be to interrogate the genes that encode the filtration bar-<lb/>rier in patients with LPHS. There are 8 genes that encode <lb/>GBM and receptors and 10 genes that code for endothelial <lb/>cells that we know of to date. 14 <lb/>While hematuria is believed to be glomerular in origin, the <lb/>genesis of the pain remains an unsolved issue. The transmis-<lb/>sion of pain from the viscera to the brain involves a pathway <lb/>that is controlled by a series of genes that code for transduc-<lb/>tion, conduction, synaptic transduction, and modulation. <lb/>Specialized receptors, expressed in the peripheral termini of <lb/>these neurons, allow noxious stimuli to be transduced into <lb/>electrical impulses. The local membrane depolarization gen-<lb/>erated by stimulus transduction is transmitted along the axon <lb/>by specific channels, some of which are expressed <lb/></body>
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+			<front>1 Dr. T. Bhanu Prasad Med Prof Corp, Regina, SK, Canada <lb/>2 Departments of Medicine and Health Research Methodology, Evidence, <lb/>and Impact, McMaster University, Hamilton, ON, Canada <lb/>3 Division of Nephrology, St Joseph&apos;s Healthcare Hamilton, ON, Canada <lb/>4 Department of Academic Family Medicine, College of Medicine, <lb/>University of Saskatchewan, Regina, Canada <lb/>5 Department of Pathology and Lab Medicine, University of Saskatchewan, <lb/>Saskatoon, Canada <lb/>6 Section of Nephrology, Department of Medicine, Regina General <lb/>Hospital, SK, Canada <lb/>7 College of Medicine, University of Saskatchewan, Regina, Canada <lb/>Corresponding Author: <lb/>Bhanu Prasad, Section of Nephrology, Department of Medicine, Regina <lb/>General Hospital, 1440, 14th Avenue, Regina, SK S4P 0W5, Canada. <lb/>Email: bprasad@sasktel.net <lb/></front>
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+			<note place="headnote">Sharma et al <lb/></note>
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+			<page>3 <lb/></page>
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+			<body>specifically in nociceptors. Transmission is modulated by <lb/>specific channels, which generally act to reduce excitability. <lb/>Nociceptors terminate in the spinal cord dorsal horn, forming <lb/>synapses with nociceptive-specific spinal projection neurons. <lb/>From the spinal cord, information is transmitted to the brain <lb/>stem and then processed by a pain matrix in multiple brain <lb/>regions. Descending input from the brain to the spinal cord <lb/>back to the periphery can both inhibit and facilitate the trans-<lb/>mission of information in nociceptive circuits. We believe <lb/>that LPHS patients have either gain-of-function mutation of <lb/>the pain pathways and/or a loss-of-function mutation in the <lb/>pain dampening pathways. We hypothesize that rare variants <lb/>identified in this study will help delineate disease pathways <lb/>from a syndrome driven by clinically ascertained phenotype <lb/>as a diagnosis of exclusion into one based on the molecular <lb/>basis of disease that leads to hematuria and physically inca-<lb/>pacitating pain (Figure 1). To improve the sensitivity and <lb/>specificity to identify a responsible variant over singleton <lb/>analysis, we decided to perform a family-based analysis. <lb/>Exome sequencing will be performed in LPHS-affected pro-<lb/>bands and participating first-degree family members, to <lb/>effectively detect de novo and compound heterozygous vari-<lb/>ants. In the absence of parents, analysis will be performed on <lb/>the other family members such as siblings or cousins. <lb/>Systematic Review of Observational <lb/>Studies <lb/>We searched PubMed, Embase, Scopus and Web of Science <lb/>databases to identify published studies on LPHS (search term: <lb/>&quot;loin pain hematuria&quot; OR &quot;Loin pain-hematuria&quot; OR &quot;loin <lb/>pain/haematuria&quot; OR &quot;loin pain haematuria&quot;). The search <lb/>was generated in September 2021, with no date limits set. A <lb/>total of 110 articles were identified. Studies with no abstracts <lb/>or articles were excluded (n = 6). Upon review of 104 LPHS <lb/>articles included, encompassing 610 LPHS patients, with <lb/>68% of the articles and 87% of patients reported from the <lb/>United States and United Kingdom alone. With all articles <lb/>published so far focusing on symptomatic pain management <lb/>using oral narcotic therapy and/or interventional management <lb/>strategies such as intra-ureteric infusions, 15-17 surgical renal <lb/>denervation, 18-20 radiofrequency ablation, 21-23 neuromodula-<lb/>tion, 24-26 and auto-transplantation, 27-31 we did not identify any <lb/>studies looking at (A) evidence of familial clustering of LPHS <lb/>or its components, variability in prevalence across different <lb/>ancestries, or antecedent exposures or condition, or (B) vari-<lb/>ants in genes coding for proteins that are involved in GEC, <lb/>GBM, or the pain pathways. <lb/>Research Objectives <lb/>The specific objectives of the study are as follows: <lb/>Objective 1: Identify potentially pathogenic variants in <lb/>18 genes associated with hematuria 14 (Table 1). <lb/>Objective 2: Identify potentially pathogenic variants in <lb/>89 genes associated with pain syndromes 32 (Table 2). <lb/>Methods <lb/>We plan to conduct a single-center, pilot study with the aim <lb/>of decoding the molecular basis of LPHS. The study has <lb/>Figure 1. Study design. <lb/></body>
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+			<page>4 <lb/></page>
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+			<note place="headnote">Canadian Journal of Kidney Health and Disease <lb/></note>
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+			<body>Table 1. Candidate Genes to be Investigated for Contributing to Hematuria in LPHS. <lb/>Gene name <lb/>Chromosome number <lb/>Inheritance a <lb/>Gene annotation <lb/>Glomerular basement membrane and receptors <lb/>LAMB2 <lb/>chr3 <lb/>AR <lb/>Laminin subunit beta 2 <lb/>LAMA5 <lb/>chr20 <lb/>AR <lb/>Laminin subunit alpha 5 <lb/>ITGA3 <lb/>chr17 <lb/>AR <lb/>Integrin subunit alpha 3 <lb/>COL4A3/4/5 <lb/>chr2/chr2/chrX <lb/>AR, AD/AR, AD/XLD <lb/>Collagen type IV alpha 3/4/5 chain <lb/>GPC5 <lb/>chr13 <lb/>Glypican 5 <lb/>CD151 <lb/>chr11 <lb/>CD151 molecule -transmembrane 4 superfamily <lb/>Endothelial cells <lb/>CFH <lb/>chr1 <lb/>AR, AD <lb/>Complement factor H <lb/>CFB <lb/>chr6 <lb/>AR, AD, DD <lb/>Complement factor B <lb/>CFI <lb/>chr4 <lb/>AR, AD <lb/>Complement factor I <lb/>C3 <lb/>chr19 <lb/>AR, AD <lb/>Complement C3 <lb/>MCP <lb/>chr1 <lb/>AR, AD <lb/>Membrane cofactor protein <lb/>THBD <lb/>chr20 <lb/>AD <lb/>Thrombomodulin <lb/>PLG <lb/>chr6 <lb/>AR, AD <lb/>Plasminogen <lb/>DGKE <lb/>chr17 <lb/>AR <lb/>Diacylglycerol kinase epsilon <lb/>INF2 <lb/>chr14 <lb/>AD <lb/>Inverted formin 2 <lb/>MMACHC <lb/>chr1 <lb/>AR <lb/>Metabolism of cobalamin associated C <lb/>a <lb/>Inheritance based on OMIM database: AD, autosomal dominant; AR, autosomal recessive; Mu, multifactorial; SMu, somatic mutation; XL, X linked; XLR, <lb/>X linked recessive; XLD, X linked dominant <lb/>Table 2. Candidate Genes to be Investigated for Understanding Pain in LPHS Patients. <lb/>Gene name <lb/>Chromosome number <lb/>Inheritance a <lb/>Gene annotation <lb/>Pain transduction <lb/>TRPV1/2/3/4 <lb/>chr17/chr17/chr17/chr12 TRPV3/4: AD <lb/>Transient receptor potential cation channel subfamily <lb/>V member 1/2/3/4 <lb/>P2RX3 <lb/>chr11 <lb/>P2X purinergic receptor <lb/>TRPM8 <lb/>chr2 <lb/>Transient receptor potential cation channel subfamily <lb/>M member 8 <lb/>TRPA1 <lb/>chr8 <lb/>AD <lb/>Transient receptor potential cation channel subfamily <lb/>A member 1 <lb/>P2RY12 <lb/>chr3 <lb/>AR <lb/>Purinergic receptor P2y12 <lb/>BDKRB1/2 <lb/>chr14/chr14 <lb/>Bradykinin receptor B1/2 <lb/>HTR3a <lb/>chr11 <lb/>5-Hydroxytryptamine receptor 3a <lb/>ACCN1/2 <lb/>chr17/chr12 <lb/>Acid sensing ion channel subunit 1/2 <lb/>TRPC/P <lb/>chr13 <lb/>Transient receptor potential canonical <lb/>Pain conduction <lb/>SCN10A <lb/>chr3 <lb/>AD <lb/>Sodium voltage-gated channel alpha subunit 10 <lb/>SCN11A <lb/>chr3 <lb/>AD <lb/>Sodium voltage-gated channel alpha subunit 11 <lb/>SCN1,3,8A <lb/>chr2/chr2/chr12 <lb/>AD/AD/AD <lb/>Sodium channel protein type 1/3/8A <lb/>SCN9A <lb/>chr2 <lb/>AR, AD <lb/>Sodium voltage-gated channel alpha subunit 9 <lb/>KCNQ <lb/>chr11 <lb/>AR, AD <lb/>Potassium voltage-gated channel subfamily Q <lb/>Pain synaptic transmission <lb/>NR1, 2 <lb/>chr9/ <lb/>AR, AD <lb/>Nuclear receptor subfamily 1/2 <lb/>GRIA1-4 <lb/>chr5/chr4/chrX/chr11 <lb/>AR, AD/ AD/ XLR/ AD <lb/>AMPA receptor 1-4 <lb/>NK1R <lb/>chr2 <lb/>Tachykinin receptor 1 <lb/>CACNA1A-I, S <lb/>chr19/chr9/chr12/chr3/ <lb/>chr1/chrX/chr17/chr16/ <lb/>chr22/chr1 <lb/>AD/ AR/ AD/ AR, AD/ AD/ <lb/>XL, XLR/ AD/ AD/ AD/ A <lb/>R, AD <lb/>Calcium voltage-gated channel subunit alpha1 A-S <lb/>CACNA2D1 <lb/>chr7 <lb/>AR <lb/>Calcium voltage-gated channel auxiliary subunit alpha2 <lb/>delta 1 <lb/>(continued) <lb/></body>
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+			<note place="headnote">Sharma et al <lb/></note>
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+			<page>5 <lb/></page>
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+			<body>Gene name <lb/>Chromosome number <lb/>Inheritance a <lb/>Gene annotation <lb/>Pain modulation <lb/>BDNF <lb/>chr11 <lb/>Brain-derived neurotrophic factor <lb/>OPRD1/M1/K1 <lb/>chr1/ chr6/ chr8 <lb/>Opioid receptor delta 1/Mu1/kappa 1 <lb/>CNR1 <lb/>chr6 <lb/>Cannabinoid receptor 1 <lb/>GABRs (GABRD/E/ <lb/>P/Q/A1-A6/BR1-<lb/>BR3/G1-G3/R1-R3 <lb/>chr1/chrX/chr5/chrX/chr5/ <lb/>chr4/chrX/chr4/chr15/ <lb/>chr5/chr4/chr5/chr15/ <lb/>chr4/chr5/chr15/chr6/ <lb/>chr6/chr3 <lb/>AD/ M/ M/ M/ AD/ AD, Mu/ <lb/>XL/ M/ AD/ M/ AD/AD/ <lb/>AD/ M/ AD/ M/ M/ M/ M <lb/>Gamma-aminobutyric acid type A receptors <lb/>TNF <lb/>chr6 <lb/>AD <lb/>Tumor necrosis factor <lb/>PLA2G2A <lb/>chr1 <lb/>AD, SMu <lb/>Phospholipase A2 <lb/>IL1/6/12/18 <lb/>chr2/chr7/chr3/chr11 <lb/>M/ Mu, SMu, AR, AD/ M/ M Interleukin 1/6/12/18 <lb/>COX2 <lb/>chrMT <lb/>Cytochrome C oxidase subunit 2 <lb/>NTRK1 <lb/>chr1 <lb/>AR <lb/>High affinity nerve growth factor receptor <lb/>NGF <lb/>chr1 <lb/>AR <lb/>Beta-nerve growth factor <lb/>GDNF <lb/>chr5 <lb/>AD <lb/>Glial cell line-derived neurotrophic factor <lb/>LIF <lb/>chr22 <lb/>AD <lb/>Leukemia inhibitory factor <lb/>CCL2 <lb/>chr17 <lb/>C-C motif chemokine 2 <lb/>CNR2 <lb/>chr1 <lb/>Cannabinoid receptor 2 <lb/>TLR2/4 <lb/>chr4/chr9 <lb/>AD, SMu/ M <lb/>Toll-like receptor 2/4 <lb/>P2RX4/7 <lb/>chr12/chr12 <lb/>P2X purinoceptor 4/7 <lb/>CX3CR1 <lb/>chr3 <lb/>CX3C chemokine receptor 1 <lb/>a <lb/>Inheritance based on OMIM database: AD, autosomal dominant; AR, autosomal recessive; Mu, multifactorial; SMu, somatic mutation; XL, X linked; XLR, <lb/>X linked recessive; M, missing or no information in OMIM database. <lb/>Table 2. (continued) <lb/>been approved by the Saskatchewan Health Authority <lb/>Research Ethics Board (REB-22-66). <lb/>Design <lb/>Number of Subjects <lb/>Twenty-four LPHS patients referred to the nephrology clinic <lb/>(run by the corresponding author) were approached by the <lb/>study coordinator, and all 24 agreed to participate in the <lb/>study. Recruitment of 2 family members of the LPHS patient <lb/>(parents/siblings/cousins/children) is ongoing. We are the <lb/>first study to identify and report 2 patients with LPHS (12, <lb/>17) with a positive family history of LPHS (Figure 2). In <lb/>addition, 6 LPHS patients (LPHS: 01, 02, 04, 05, 11, and 21) <lb/>had a positive family history of intermittent hematuria <lb/>(Figure 2). <lb/>Duration of Study Period <lb/>The study period extended for about 3 years (2022-2025). <lb/>Participant Selection and Informed Consent <lb/>The LPHS patients have been identified by BP (Nephrologist) <lb/>and FG (Urologist), based on the inclusion and exclusion cri-<lb/>teria defined by Spetie et al 4 All patients and family mem-<lb/>bers that meet the eligibility criteria will need to complete <lb/>the written consent forms followed by baseline data collec-<lb/>tion (detailed below). <lb/>Inclusion criteria for LPHS patient <lb/>• <lb/>• ≥18 years of age <lb/>• <lb/>• Patients diagnosed with LPHS (by nephrologist and/ <lb/>or urologist). <lb/>Exclusion criteria for LPHS patient <lb/>• <lb/>• Urological causes of flank pain and hematuria <lb/>(obstructive uropathy, nephrolithiasis, pyelonephritis, <lb/>polycystic kidney disease, renal artery embolism, <lb/>renal artery dissection, renal papillary necrosis, renal <lb/>vein thrombosis, left renal vein entrapment [nut-<lb/>cracker syndrome], renal trauma, or renal tumor). <lb/>• <lb/>• Additional functional/structural reason for hematuria <lb/>by kidney biopsy or other interventions. <lb/>Inclusion/exclusion criteria for family members <lb/>• <lb/>• Only family members (parents/siblings/children/first <lb/>cousin) of the patient who provide informed consent. <lb/>Data Collection, Sample Collection, <lb/>and Exome Analysis <lb/>Demographic Data <lb/>Data related to age, sex, gender, self-reported race/ethnic-<lb/>ity, occupation, socioeconomic status, weight, height, <lb/></body>
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+			<page>6 <lb/></page>
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+			<note place="headnote">Canadian Journal of Kidney Health and Disease <lb/></note>
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+			<body>Figure 2. Pedigree of LPHS patients with a family history of LPHS or isolated hematuria (IH). Roman numbers represent the <lb/>generations of the family. <lb/>Note. Proband is indicated by arrow. Abbreviations: k, kidney stones; m, migraine. <lb/>comorbidities, family history of diseases (eg, kidney stones, <lb/>isolated hematuria, LPHS, diabetes, hypertension, chronic <lb/>fatigue syndrome, mood disorders, asthma, and allergies), <lb/>the location of pain (bilateral or unilateral), the number and <lb/>frequency of pain medications, and pain score using the brief <lb/>pain inventory form and PainDetect questionnaire will be <lb/>collected for the LPHS patients. <lb/>Laboratory Data <lb/>Complete blood count, serum electrolytes, serum urea and <lb/>creatinine, albumin creatinine ratio, and urine analysis. <lb/>Genetic Data <lb/>Rare variants in genes associated with hematuria (n = 18) <lb/>and in pain transduction (n = 17), conduction (n = 8), syn-<lb/>aptic transmission (n = 37), and pain modulation (n = 27). <lb/>Hierarchical Clustering of Patient Phenotype Data <lb/>Patients will be grouped based on their demographic, labora-<lb/>tory, and genetic data using unsupervised hierarchical clus-<lb/>tering (Ward&apos;s method with Euclidean distances). 33 The data <lb/>will be presented as clustered dendrograms. <lb/>Sample Collection, Storage, and Preparation <lb/>Venous blood samples will be collected for study probands <lb/>and participating family members in PAXgene Blood RNA <lb/>Tubes (Qiagen, Hilden, Germany). DNA will be extracted <lb/>from PAXgene Blood RNA Tube using the New England <lb/>Biolabs Monarch Genomic DNA Purification Kit as per the <lb/>protocol by Kruhøffer et al. 34 DNA libraries will be con-<lb/>structed using the Illumina DNA Prep with Enrichment, <lb/>Tagmentation kit and IDT xGen Exome Research Panel v2 <lb/>with xGen Universal Blockers-NXT Mix and dual unique <lb/></body>
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+			<note place="headnote">Sharma et al <lb/></note>
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+			<page>7 <lb/></page>
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+			<body>barcodes. Paired-end sequencing (2 × 150 bps) on the <lb/>Illumina NovaSeq 6000 System at 100× depth for exome <lb/>sequencing. Library preparation and sequencing will be per-<lb/>formed for all family members at the same time to minimize <lb/>potential artifactual differences due to sample preparation. <lb/>DNA samples will be stored at -80° centigrade to allow for <lb/>future verification studies. <lb/>Exome Analysis <lb/>As depicted in Figure 3, raw fastq files will be processed to <lb/>remove adapter sequences using cutadapt (v1.11). 35 Reads <lb/>with quality score of ≥30 will be retained for analysis. <lb/>Contaminating reads will be removed after aligning of the <lb/>processed reads to the human genome using BWA 36 and <lb/>Samtools. 37 The reads will be preprocessed using the <lb/>Genomic Analysis Tool Kit (GATK), as per the recommen-<lb/>dations in the Best Practices Workflow by the GATK 38 for all <lb/>positions with ≥20× coverage, genotype quality ≥20, and <lb/>minor read ratio ≥0.2 for indel alignment, base quality score <lb/>recalibration, base alignment quality scoring, and variant <lb/>calling (single-nucleotide variants [SNVs], indels, short tan-<lb/>dem repeats [STRs], structural variant [SV]). Variant allele <lb/>frequency (VAF) will be calculated as the percentage of <lb/>sequence reads observed for the alternative allele compared <lb/>to all coverage of that nucleotide. Exome data will first be <lb/>evaluated for genes associated with isolated hematuria and <lb/>pain (as listed in Tables 1 and 2). The variants will be further <lb/>filtered and prioritized using VarSeq software (Golden Helix, <lb/>Bozeman, MT, USA) and variant effect predictor. Benign <lb/>variants with MAF (minor allele frequency) &gt;1% in any <lb/>ancestry will be eliminated using the 1000 Genomes <lb/>Project, 39 dbSNP, 40 gnomAD 41 and National Institutes of <lb/>Health (NIH)&apos;s All of Us. 42 In silico bioinformatic prediction <lb/>of pathogenicity of variants will be performed using the fol-<lb/>lowing prediction algorithms: scale-invariant feature trans-<lb/>form (SIFT), 43 PolyPhen2, 44 Mutation Taster, 45 CADD, 46 <lb/>VEST, 47 and FATHMM. 48 Finally, the candidate variants will <lb/>be checked against the human gene mutation database <lb/>(HGMD) 41 , LOVD, 12 Clinvar, 49 and Alport database. 50 A <lb/>multidisciplinary team will then review each variant for evi-<lb/>dence of pathogenicity and contribution to the phenotype <lb/>and classify them according to the American College of <lb/>Medical Genetics guidelines. 51 Possible pathogenic loci will <lb/>be screened according to 3 heredity models, namely autoso-<lb/>mal recessive (AR) inheritance, autosomal dominant (AD), <lb/>and X-linked inheritance. Sanger sequencing will be carried <lb/>out to validate potentially pathogenic variants identified <lb/>through high-throughput exome sequencing. Special atten-<lb/>tion will be paid to de novo variants, not present in parents, <lb/>as well as variants with variant allele frequencies suggestive <lb/>of potential somatic variation. Finally, we will also assess for <lb/>the presence of copy number variation using CoNIFER, 52 <lb/>cn.MOPS, 53 and CNVkit. 54 To evaluate the pathogenicity of <lb/>a rare variant, we will look at the segregation of variants <lb/>among all sequenced family members using (A) probability-<lb/>based models by Helbig et al 55 and Jarvik et al, 56 and (B) <lb/>gene-based segregation methods. 57 <lb/>Potential Risks to the Participants <lb/>In Canada, people are protected from being required to <lb/>provide the results of a genetic test by the Genetic Non-<lb/>Discrimination Act. 58 The genetic results will not be <lb/>Figure 3. Pipeline for exome data analysis. <lb/></body>
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+			<page>8 <lb/></page>
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+			<note place="headnote">Canadian Journal of Kidney Health and Disease <lb/></note>
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+			<body>disclosed to any third party such as employers, insurance <lb/>companies, or educational institutions. The confidentiality of <lb/>the participant will be respected. All collected samples will <lb/>be assigned a unique study number, with no reference to indi-<lb/>vidual identifiers. As this research involves looking at genetic <lb/>information, it carries the risk of identifying an underlying <lb/>genetic change(s) which are unrelated to this study and have <lb/>the potential of affecting the participant. However, this <lb/>research is being conducted for the scientific purpose of <lb/>understanding only the cause of pain and hematuria in LPHS <lb/>patients. In addition, the results of this research project will <lb/>not be placed in the participant&apos;s medical record. All efforts <lb/>will be made to safeguard participants&apos; privacy. <lb/></body>
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+			<div type="annex">Author Contributions <lb/>BP conceived and designed the study. AS wrote the initial draft. <lb/>ML and SL assisted with the drafts. ML provided advice regarding <lb/>genetic study design. BP edited the final manuscript. All authors <lb/>read and approved the final manuscript. <lb/>Declaration of Conflicting Interests <lb/>The author(s) declared the following potential conflicts of interest <lb/>with respect to the research, authorship, and/or publication of this <lb/>article: BP has received speaker and advisory fees from Bayer, <lb/>Otsuka and Astra Zeneca. MBL has received speaker and advisory <lb/>fees from Otsuka, Reata, Bayer, and Sanofi Genzyme. <lb/></div>
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+			<div type="funding">Funding <lb/>The author(s) disclosed receipt of the following financial support <lb/>for the research, authorship, and/or publication of this article: The <lb/>author(s) received financial support for the research, authorship, <lb/>and/or publication of this article from the Hospitals of Regina <lb/>Foundation. MBL has funding support from CIHR project grant <lb/>(grant no. 201909-PJT). The funding sources had no role in the <lb/>design, conduct, and analysis of the study or in the decision to sub-<lb/>mit the manuscript for publication. <lb/></div>
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+			<div type="annex">Ethics Approval and Consent to Participate <lb/>The study will be conducted in accordance with the second edition <lb/>of the Tri-Council Policy Statement-Ethical Conduct for Research <lb/>Involving Humans-TCPS 2. We have received REB certificate of <lb/>approval for the study (REB-22-66). Written informed consent will <lb/>be obtained from all the participants in the study. <lb/>Consent for Publication <lb/>Not applicable as there is no patient identifying information in this <lb/>article. <lb/></div>
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+			<div type="availability">Availability of Data and Materials <lb/>The data sets used and/or analyzed during the current study are <lb/>available from the corresponding author on reasonable request. <lb/></div>
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+			<front>ORCID iDs <lb/>Matthew B. Lanktree <lb/>https://orcid.org/0000-0002-5750-6286 <lb/>Bhanu Prasad <lb/>https://orcid.org/0000-0002-1139-4821 <lb/></front>
+
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