Figure 1.

Figure 2.

Figure 3.

Designed PCR primer sequences used in the confirmation and segregation analyses_
| Gene | Variant | Primer name | Primer nucleotide sequence (5′>3′) | PCR length (nt) |
|---|---|---|---|---|
| CPLANE1 | c.1819delT | CPLANE1_c.1819_F | CCACCAATGAGTCTTGAGCTG | 732 |
| CPLANE1_c.1819_R | AAGAACGCCAAAGTGATGCTAT | |||
| c.7817T>A | CPLANE1_c.7817_F | TGGGTTTGTAGGAGGAGAGGT | 471 | |
| CPLANE1_c.7817_R | CATACTTCCTGCTCCTTTTCCT | |||
| c.5820+3_5820+6del | CPLANE1_c.5820_F | GCCACACAGCATGGCTATATT | 431 | |
| CPLANE1_c.5820_R | TCTCAAGGCTCATCTGGGAT | |||
| DHCR7 | c.452G>A | DHCR7_c.452_F | GTGAAGCAAGTTCCATCCCC | 586 |
| DHCR7_c.452_R | GCAGAACCAAAGGATGGACTC | |||
| c.964-1G>C | DHCR7_c.964-1_F | GCAGAACACGCTCTTGACAG | 721 | |
| DHCR7_c.964-1_R | CAGGTAGAAGGCAGGTAGAGTT | |||
| RBM8A | c.-21G>A | RBM8A_ex1_F | TGAAGGGGGCGGAATCTCTA | 353 |
| RBM8A_ex1_R | TGCGTGTTTTTACCGTGCAG | |||
| NF1 | c.4537C>T | NF1_ex35_F | TGGTCCTGAGGTCTTTTTGG | 560 |
| NF1_ex35_R | TGTTGTCTTCACTCCCTGGT | |||
| F5 | c.1601G>A | FV-Leiden_F | TGATGCCCAGTGCTTAACAA | 265 |
| FV-Leiden_R | TCACACTGGTGCTAAAAAGGA | |||
| TSC1 | c.3113_3119del | TSC1_ex23_F | GGCTCTCAGAAAGGCTACTGG | 436 |
| TSC1_ex23_R | CATCCTCCGAATGTGGACAG | |||
| VWF | c.3797C>T | VWF_ex28_F | ACCGGGATCACAATGACCTT | 632 |
| VWF_ex28_R | GTAGGGCTCAGAAGTGTCCA | |||
| SLC6A1 | c.740C>A | SLC6A1_ex8_F | AAATGTGAGCTGGTTGGCTC | 432 |
| SLC6A1_ex8_R | AAACCTGGTCTACAGTGAGGG | |||
| DSG2 | c.2315del | DSG2_ex14_F | GCCCACTTGACTCAGATCCT | 590 |
| DSG2_ex14_R | TGGGTCCCATTTCTCTTTCCTTA | |||
| DVL1 | c.1961dup | DLV1_ex15_F | GGTTGTTCTGGACGTGGC | 722 |
| DLV1_ex15_R | GGTCTTCCTCATCCCAGGAG | |||
| RPGRIP1L | c.2771G>A | RPGRIP1L_2771G_A_F | GGGGTGGCAGCTTAGTTCTT | 389 |
| RPGRIP1L_2771G_A_R | CCTGGCTAGTTCACATGGTAG | |||
| c.3295-2A>G | RPGRIP1L_3295-2_F | AGGCCAATGGGCTTCTTTTCT | 3211 | |
| RPGRIP1L_3295-2_R | GATGGTGATGTCATCGGCTG | |||
| RPGRIP1L_3295-2_seq | GCAGAGGTGGGCGGATCATGAG | |||
| PAH | c.842C>T | PAH_ex7_F | GCCAGCAATGAACCCAAACC | 239 |
| PAH_ex7_R | TCTTTTCATCCCAGCTTGCAC | |||
| c.*19G>T | PAH_ex13_F | ACAAGTGGCCCATTTTGATGGT | 402 | |
| PAH_ex13_R | GGCCCATTTTGATGGTGTTTT | |||
| GBA | c.1444G>T | GBA_ex10_F | CTGCCTCTCCCACATGTGA | 391 |
| GBA_ex10_R | CAAAAGGGGATGGGTGTGC | |||
| c.1226A>G | GBA_EX9_F | CTTTTCTGCATCGCAGTCCA | 459 | |
| GBA_EX9_R | TCCCACATGTGACCCTTACC | |||
| PKHD1 | c.107C>T | PKHD1_ex3_F | CAGGCCCACTTTTACACCTG | 423 |
| PKHD1_ex3_R | GGGGCTTCTGATGATGTGTTT | |||
| c.10883C>T | PKHD1_ex61_F | ATCAGCCCTCATTTGGATGTGA | 537 | |
| PKHD1_ex61_R | TTCCATTCACTTGGCCCTCA | |||
| PRDM6 | c.1057G>A | PRDM6_ex5_F | ATTGGTTGCTGGGGACAATC | 380 |
| PRDM6_ex5_R | AGTGAACCACGTTTCATGAGT | |||
| TBX18 | c.1570C>T | TBX18_ex8_F | GCAACTGGATGAAACAGGGG | 1074 |
| TBX18_ex8_R | CTCCAACCCTTGCCTTGTAAC | |||
| SCN5A | c.3911C>T | SCN5A_ex22_F | CACGGCCATAGGACATCAGA | 268 |
| SCN5A_ex22_R | TGTTCCCATCCTCCCCATTT | |||
| MYH3 | c.3137G>A | MYH3_ex25_F | TCTTCTGAAACTGGAGGCCC | 345 |
| MYH3_ex25_R | CTTGCAAAGCATTTGTTCCCA |
Zygosity, inheritance, OMIM-associated diseases, and interpretive grouping of the detected genes
| Case | Gene | Variant | Accession number | AF (gnomAD) | Internal frequency | OMIM disease/s; Inheritance | Major developmental / organ system |
|---|---|---|---|---|---|---|---|
| 1. Genes plausibly associated with prenatal or early embryonic lethality | |||||||
| Definitive molecular diagnoses | |||||||
| Abp-411 | CPLANE1 | c.1819delT;7817T>A | rs777686211; rs749523755 | 0.0001554; 0.00002390 | 0.0077 | 614615, Joubert Syndrome 17, AR; 277170, Orofaciodigital syndrome VI, AR | Multi-system |
| Abp-4451 | CPLANE1 | c.1819delT;7817T>A | rs777686211; rs749523755 | 0.0001554; 0.00002390 | 0.0077 | 614615, Joubert Syndrome 17, AR; 277170, Orofaciodigital syndrome VI, AR | Multi-system |
| c.5820+3_5820+6del | / | / | 0.0017 | ||||
| Abp-4942 | DHCR7 | c.452G>A | rs11555217 | 0.0007759 | 0.0084 | 270400, Smith-Lemli-Opitz syndrome, AR | Multi-system |
| c.964-1G>C | rs138659167 | 0.003854 | 0.0042 | ||||
| Abp-5452 | DHCR7 | c.452G>A | rs11555217 | 0.0007759 | 0.0084 | 270400, Smith-Lemli-Opitz syndrome, AR | Multi-system |
| c.964-1G>C | rs138659167 | 0.003854 | 0.0042 | ||||
| Abp-5511 | CPLANE1 | c.1819delT;7817T>A | rs777686211; rs749523755 | 0.0001554; 0.00002390 | 0.0077 | 614615, Joubert Syndrome 17, AR; 277170, Orofaciodigital syndrome VI, AR | Multi-system |
| c.5820+3_5820+6del | / | / | 0.0017 | ||||
| Possible monogenic contributors | |||||||
| Abp-501 | GBA1 | c.1444G>T | / | / | 0 | 608013, 230800, 230900, 231000, 231005, Gaucher disease types perinatal death, I, II, III, IIIC, AR | Multi-system |
| c.1226A>G | rs76763715 | 0.002235 | 0.0067 | ||||
| Abp-694 | PKHD1 | c.107C>T | rs137852944 | 0.0005094 | 0.0014 | 263200, Polycystic kidney disease 4, with or without hepatic disease, AR | Kidney anomalies |
| c.10883C>T | rs147700643 | 0.00005312 | 0 | ||||
| Abp-825 | RPGRIP1L | c.2771G>A | rs142234650 | / | 0 | 611561, Meckel syndrome 5, AR; 611560, Joubert syndrome 7, AR | Ciliopathies/multi-system |
| c.3295-2A>G | rs1258182460 | / | 0 | ||||
| 2. Genes causing severe congenital disorders not typically considered embryonically lethal | |||||||
| Definitive molecular diagnoses | |||||||
| Abp-251 | SLC6A1 | c.740C>A | / | / | 0 | 616421, Myoclonic-atonic epilepsy, AD | Neurologic |
| Abp-716 | RBM8A | c.-21G>A | rs139428292 | 0.01794 | >2% | 274000, Thrombocytopenia-absent radius syndrome, AR | Multi-system |
| 1q21.1-q21.2 | chr1:143,767,833-149,400,542 | / | / | 0 | |||
| Abp-799 | NF1 | c.4600C>T | rs760703505 | 0.000007957 | 0 | 162200, Neurofibromatosis, type 1, AD | Multi-system |
| Abp-801 | DSG2 | c.2315del | / | / | 0 | 610193, Arrhythmogenic right ventricular dysplasia 10, AD | Cardiac |
| Abp-825 | DVL1 | c.1961dup | / | / | 0 | 616331, Robinow syndrome, autosomal dominant 2, AD | Skeletal |
| Possible monogenic contributors | |||||||
| Abp-80 | PAH | c.842C>T | rs5030851 | 0.0001026 | 0.0010 | 261600, Phenylketonuria, AR | Metabolic |
| c.*19G>T | rs372637021 | 0.002029 | 0 | ||||
| Abp-87 | PRDM6 | c.1057G>A | rs202224762 | 0.0002604 | 0.0010 | 617039, Patent ductus arteriosus 3, AD | Cardiac |
| Abp-166 | TBX18 | c.1570C>T | rs760905589 | 0.000008061 | 0.0010 | 143400, Congenital anomalies of kidney and urinary tract 2, AD | Kidney anomalies |
| Abp-233 | SCN5A | c.3911C>T | rs199473603 | 0.0001649 | 0 | 601144, Brugada syndrome 1, AD; 601154, Cardiomyopathy, dilated, 1E, AD; 603830, Long QT syndrome 3, AD | Cardiac |
| Abp-577 | TSC1 | c.3113_3119del | / | / | 0.00035 | 191100, Tuberous sclerosis-1, AD | Multi-system |
| Abp-781 | MYH3 | c.3137G>A | rs142002449 | 0.0004031 | 0.0010 | 193700, Arthrogryposis, distal, type 2A (Freeman-Sheldon), AD | Skeletal |
| 3. Genes linked to later-onset or susceptibility phenotypes | |||||||
| Abp-668 | VWF | c.3797C>T | rs61749370 | 0.0008322 | 0.0010 | 193400, von Willebrand disease, AD/AR | Blood |
| Abp-809 | F5 | c.1601G>A | rs6025 | 0.01752 | >3% | 188055, Thrombophilia 2 due to activated protein C resistance, AD; 614389, {Pregnancy loss, recurrent, susceptibility to, 1}, AD | Blood |
| Additional distinct pathogenic copy-number finding | |||||||
| Abp-972 [U] | 21q22.12-q22.3 | chr21:33,398,108–43,587,648 | / | / | 0 | /, 21q22 Duplication Syndrome | Multi-system |
Detailed overview of variants detected by WES in euploid EPL and their molecular characteristics
| Case | Gene | Reference sequence | Variant | Protein change | Zygosity | Inheritance | Type of variant | Known / Novel | ACMG classification | ACMG criteria |
|---|---|---|---|---|---|---|---|---|---|---|
| 1. Genes plausibly associated with prenatal or early embryonic lethality | ||||||||||
| Definitive molecular diagnoses | ||||||||||
| Abp-411 | CPLANE1 | NM_001384732.1 | c.1819delT;7817T>A | p.Tyr607ThrfsTer6; p.Leu2624Ter | hom | M/F | Frameshift | Known | Pathogenic | PVS1; PM2; PP5/PVS1; PM2; PP5 |
| Abp-445 1 | CPLANE1 | NM_001384732.1 | c.1819delT;7817T>A | p.Tyr607ThrfsTer6; p.Leu2624Ter | het | F | Frameshift; Nonsense | Known | Pathogenic | PVS1; PM2; PP5/PVS1; PM2; PP5 |
| c.5820+3_5820+6del | exon 29 skipping | het | M | Splice site | Novel | Pathogenic | PS3, PM2; PM3; PM4; PP3 | |||
| Abp-4942 | DHCR7 | NM_001360.3 | c.452G>A | p.Trp151Ter | het | F | Nonsense | Known | Pathogenic | PVS1; PM2; PP5 |
| c.964-1G>C | altered splicing | het | M | Splice site | Known | Pathogenic | PVS1; PM2; PP5 | |||
| Abp-5452 | DHCR7 | NM_001360.3 | c.452G>A | p.Trp151Ter | het | F | Nonsense | Known | Pathogenic | PVS1; PM2; PP5 |
| c.964-1G>C | altered splicing | het | M | Splice site | Known | Pathogenic | PVS1; PM2; PP5 | |||
| Abp-5511 | CPLANE1 | NM_001384732.1 | c.1819delT;7817T>A | p.Tyr607ThrfsTer6; p.Leu2624Ter | het | F | Frameshift; Nonsense | Known | Pathogenic | PVS1; PM2; PP5/PVS1; PM2; PP5 |
| c.5820+3_5820+6del | exon 29 skipping | het | M | Splice site | Novel | Pathogenic | PVS1; PM2; PP5/PVS1; PM2; PP5 | |||
| Possible monogenic contributors | ||||||||||
| Abp-501 | GBA1 | NM_000157.4 | c.1444G>T | p.Asp482Tyr | het | M | Missense | Known | VUS | PM2; PM3; PP3 |
| c.1226A>G | p.Asn409Ser | het | F | Missense | Known | Likely pathogenic | PM1; PM2; PM5; PP2; PP3; PP5 | |||
| Abp-694 | PKHD1 | NM_138694.4 | c.107C>T | p.Thr36Met | het | M | Missense | Known | Likely pathogenic | PM2; PM5; PP3; PP5 |
| c.10883C>T | p.Thr362Ile | het | F | Missense | Known | VUS | PM2; PM3 | |||
| Abp-825 | RPGRIP1L | NM_015272.5 | c.2771G>A | p.Ser924Asn | het | M | Missense | Known | VUS | PM2, PM3 |
| c.3295-2A>G | / | het | F | Splice site | Known | Likely pathogenic | PVS1; PM2; PP5 | |||
| 2. Genes causing severe congenital disorders not typically considered embryonically lethal | ||||||||||
| Definitive molecular diagnoses | ||||||||||
| Abp-251 | SLC6A1 | NM_003042.4 | c.740C>A | p.Pro247His | het | de novo | Missense | Novel | Likely pathogenic | PM2; PM5; PP2; PP3 |
| Abp-716 | RBM8A | NM_005105.5 | c.-21G>A | / | het | M | Missense/noncoding | Known | Pathogenic, low penetrance | PS3, PM3 |
| 1q21.1-q21.2 | hg19 | chr1:143,767,833-149,400,542 | / | het | F | Deletion | Known | Pathogenic | 2A; 3B; 4L >1 point | |
| Abp-799 | NF1 | NM_001042492.3 | c.4600C>T | p.Arg1513Ter | het | F | Nonsense | Known | Pathogenic | PVS1; PM2; PP5 |
| Abp-801 | DSG2 | NM_001943.5 | c.2315del | p.Leu772Ter | het | M | Nonsense | Novel | Likely pathogenic | PVS1; PM2 |
| Abp-825 | DVL1 | NM_001330311.2 | c.1961dup | p.Pro657AlafsTer50 | het | F | Frameshift | Novel | Likely pathogenic | PVS1; PM2 |
| Possible monogenic contributors | ||||||||||
| Abp-80 | PAH | NM_000277.3 | c.842C>T | p.Pro281Leu | het | M | Missense | Known | Pathogenic | PS3, PM2; PM5; PP2; PP3; PP5 |
| c.*19G>T | / | het | F | Missense/noncoding | Known | VUS | PM3; BS1; BS2; BP7 | |||
| Abp-87 | PRDM6 | NM_001136239.4 | c.1057G>A | p.Asp353Asn | het | M | Missense | Known | VUS | PM2 |
| Abp-166 | TBX18 | NM_001080508.3 | c.1570C>T | p.His524Tyr | het | M | Missense | Known | VUS | PM2; PP3; PP5 |
| Abp-233 | SCN5A | NM_000335.5 | c.3911C>T | p.Thr1304Met | het | F | Missense | Known | VUS | PM2, PP3, PP5 |
| Abp-577 | TSC1 | NM_000368.5 | c.3113_3119del | p.Ser1038ThrfsTer51 | het | F | Frameshift | Novel | VUS | PVS1(moderate); PM2 |
| Abp-781 | MYH3 | NM_002470.4 | c.3137G>A | p.Arg1046Gln | het | M | Missense | Known | VUS | PM2; PP3 |
| 3. Genes linked to later-onset or susceptibility phenotypes | ||||||||||
| Abp-668 | VWF | NM_000552.5 | c.3797C>T | p.Pro1266Leu | het | M | Missense | Known | Likely pathogenic | PM1; PM2; PM5; PP5 |
| Abp-809 | F5 | NM_000130.5 | c.1601G>A | p.Arg534Gln | hom | M (hom)/F (het) | Missense | Known | Pathogenic, low penetrance | PS3, PS4 |
| Additional distinct pathogenic copy-number finding | ||||||||||
| Abp-972 | 21q22.12-q22.3dup | hg19 | chr21:33,398,108-43,587,648 | / | het | de novo | Duplication | Known | Pathogenic | 3C; 4L >1 point |
Detailed overview of the demographic and clinical characteristics of the EPL studied group
| Sample ID | Fetal sex | Ethnic origin | Gestational age (weeks) | Maternal Age | No. of PLs (n) | Livebirths (n) | |
|---|---|---|---|---|---|---|---|
| 1 | Abp-2 | F | MKD | 8 | 42 | 4 | 1 |
| 2 | Abp-26 | F | ALB | 7 | 30 | 5 | 0 |
| 3 | Abp-76 | M | MKD | 8 | 31 | 3 | 0 |
| 4 | Abp-80 | F | ALB | 6 | 26 | 6 | 0 |
| 5 | Abp-87 | M | ALB | 9 | 29 | 4 | 1 |
| 6 | Abp-166 | F | ALB | 7 | 38 | 12 | 0 |
| 7 | Abp-233 | F | MKD | 8 | 40 | 4 | 0 |
| 8 | Abp-251 | M | MKD | 8 | 29 | 4 | 0 |
| 9 | Abp-2581 | F | MKD | 8 | 31 | 11 | 0 |
| 10 | Abp-266 | F | MKD | 7 | 32 | 4 | 0 |
| 11 | Abp-2722 | M | ALB | 11 | 28 | 4 | 0 |
| 12 | Abp-278 | F | ALB | 9 | 24 | 4 | 2 |
| 13 | Abp-303 | F | ALB | 8 | 29 | 2 | 0 |
| 14 | Abp-312 | M | ALB | 12 | 27 | 3 | 1 |
| 15 | Abp-357 | M | MKD | 9 | 41 | 3 | 0 |
| 16 | Abp-367 | M | ALB | 8 | 30 | 3 | 0 |
| 17 | Abp-3722 | M | ALB | 9 | 29 | 6 | 0 |
| 18 | Abp-395 | M | MKD | 9 | 27 | 3 | 1 |
| 19 | Abp-404 | M | ALB | 7 | 28 | 3 | 0 |
| 20 | Abp-407 | M | ALB | 8 | 35 | 3 | 0 |
| 21 | Abp-411 | M | ALB | 8 | 30 | 5 | 0 |
| 22 | Abp-4443 | F | MKD | 9 | 27 | 2 | 0 |
| 23 | Abp-4454 | F | ALB | 10 | 24 | 2 | 0 |
| 24 | Abp-4575 | M | ALB | 9 | 27 | 3 | 0 |
| 25 | Abp-488 | M | ALB | 8 | 34 | 3 | 1 |
| 26 | Abp-494 | M | MKD | 7 | 32 | 3 | 0 |
| 27 | Abp-501 | F | ALB | 8 | 31 | 7 | 0 |
| 28 | Abp-5176 | F | ALB | 8 | 25 | 1 | 0 |
| 29 | Abp-5514 | F | ALB | 8 | 25 | 3 | 0 |
| 30 | Abp-562 | M | ALB | 6 | 32 | 3 | 0 |
| 31 | Abp-577 | F | MKD | 8 | 41 | 3 | 1 |
| 32 | Abp-5897 | F | MKD | 8 | 36 | 2 | 0 |
| 33 | Abp-5901 | M | MKD | 8 | 35 | 13 | 0 |
| 34 | Abp-591 | F | MKD | 8 | 35 | 4 | 0 |
| 35 | Abp-6013 | F | MKD | 8 | 28 | 3 | 0 |
| 36 | Abp-604 | M | ALB | 9 | 29 | 4 | 0 |
| 37 | Abp-642 | F | ALB | 9 | 25 | 3 | 0 |
| 38 | Abp-6565 | M | ALB | 7 | 29 | 4 | 0 |
| 39 | Abp-6657 | M | MKD | 7 | 37 | 3 | 0 |
| 40 | Abp-666 | M | MKD | 7 | 33 | 4 | 0 |
| 41 | Abp-668 | M | MKD | 10 | 37 | 2 | 0 |
| 42 | Abp-677 | F | MKD | 8 | 31 | 4 | 0 |
| 43 | Abp-682 | F | ALB | 9 | 26 | 2 | 0 |
| 44 | Abp-694 | M | ALB | 9 | 23 | 2 | 0 |
| 45 | Abp-699 | M | MKD | 12 | 29 | 2 | 0 |
| 46 | Abp-715 | F | ALB | 8 | 26 | 4 | 0 |
| 47 | Abp-716 | F | MKD | 9 | 31 | 2 | 0 |
| 48 | Abp-722 | M | MKD | 6 | 34 | 3 | 0 |
| 49 | Abp-729 | F | MKD | 8 | 36 | 2 | 0 |
| 50 | Abp-734 | M | ALB | 7 | 24 | 3 | 1 |
| 51 | Abp-741 | M | ALB | 9 | 22 | 3 | 0 |
| 52 | Abp-746 | M | MKD | 8 | 32 | 2 | 1 |
| 53 | Abp-781 | F | MKD | 9 | 33 | 2 | 0 |
| 54 | Abp-786 | F | ALB | 8 | 27 | 2 | 0 |
| 55 | Abp-799 | M | MKD | 8 | 35 | 4 | 1 |
| 56 | Abp-801 | F | MKD | 8 | 25 | 2 | 1 |
| 57 | Abp-809 | M | ALB | 12 | 20 | 3 | 0 |
| 58 | Abp-812 | F | MKD | 6 | 36 | 3 | 1 |
| 59 | Abp-8136 | M | ALB | 8 | 30 | 3 | 0 |
| 60 | Abp-825 | F | MKD | 7 | 37 | 3 | 1 |
| 61 | Abp-833 | F | MKD | 7 | 39 | 2 | 0 |
| 62 | Abp-859 | M | ALB | 8 | 31 | 2 | 3 |
| 63 | Abp-864 | M | ALB | 9 | 24 | 3 | 0 |
| 64 | Abp-866 | F | MKD | 8 | 42 | 3 | 1 |
| 65 | Abp-900 | M | MKD | 8 | 37 | 2 | 0 |
| 66 | Abp-972 | F | ALB | 9 | 31 | 4 | 1 |
PCR mixture and cycling conditions used for Sanger sequencing for confirmation and phasing of the detected variants on WES analysis_
| PCR master mix content: | Volume (ul) |
|---|---|
| H2O | 16.1 |
| 10xB2 buffer | 2.5 |
| 25mM MgCl2 | 1.3 |
| 2.5 mM nucleotide mix | 2 |
| 10mM Forward primer | 1 |
| 10 mM Reverse primer | 1 |
| HotFire Polymerase 1U/ul | 0.1 |
| DNA (100ng/ul) | 1 |
| Total volume: | 25 |
| PCR cycling conditions: | |
| 95°C/15 min | x1 cycle |
| 95°C/30 sec | x33 cycles |
| 59°C/30 sec | |
| 72°C/45 sec | |
| 72°C/10 min | x1 cycle |