Monogenic Findings in Early Pregnancy Loss: Whole-Exome Sequencing Study of Euploid Products of Conception

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
Abp-445 ¹	CPLANE1	NM_001384732.1	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
Abp-494²	DHCR7	NM_001360.3	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
Abp-545²	DHCR7	NM_001360.3	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
Abp-551¹	CPLANE1	NM_001384732.1	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
Abp-501	GBA1	NM_000157.4	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
Abp-694	PKHD1	NM_138694.4	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
Abp-825	RPGRIP1L	NM_015272.5	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
Abp-716	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
Abp-80	PAH	NM_000277.3	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

1,2 fetuses from same family. Abp-825 harbored two distinct reportable findings assigned to different interpretive categories: a heterozygous likely pathogenic DVL1 variant and a biallelic RPGRIP1L finding composed of one likely pathogenic splice-site variant and one missense VUS.

Table 2.

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
Abp-445¹	CPLANE1	c.5820+3_5820+6del	/	/	0.0017		Multi-system
Abp-494²	DHCR7	c.452G>A	rs11555217	0.0007759	0.0084	270400, Smith-Lemli-Opitz syndrome, AR	Multi-system
Abp-494²	DHCR7	c.964-1G>C	rs138659167	0.003854	0.0042	270400, Smith-Lemli-Opitz syndrome, AR	Multi-system
Abp-545²	DHCR7	c.452G>A	rs11555217	0.0007759	0.0084	270400, Smith-Lemli-Opitz syndrome, AR	Multi-system
Abp-545²	DHCR7	c.964-1G>C	rs138659167	0.003854	0.0042	270400, Smith-Lemli-Opitz syndrome, AR	Multi-system
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
Abp-551¹	CPLANE1	c.5820+3_5820+6del	/	/	0.0017		Multi-system
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
Abp-501	GBA1	c.1226A>G	rs76763715	0.002235	0.0067		Multi-system
Abp-694	PKHD1	c.107C>T	rs137852944	0.0005094	0.0014	263200, Polycystic kidney disease 4, with or without hepatic disease, AR	Kidney anomalies
Abp-694	PKHD1	c.10883C>T	rs147700643	0.00005312	0		Kidney anomalies
Abp-825	RPGRIP1L	c.2771G>A	rs142234650	/	0	611561, Meckel syndrome 5, AR; 611560, Joubert syndrome 7, AR	Ciliopathies/multi-system
Abp-825	RPGRIP1L	c.3295-2A>G	rs1258182460	/	0		Ciliopathies/multi-system
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
Abp-716	1q21.1-q21.2	chr1:143,767,833-149,400,542	/	/	0	274000, Thrombocytopenia-absent radius syndrome, AR	Multi-system
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
Abp-80	PAH	c.*19G>T	rs372637021	0.002029	0	261600, Phenylketonuria, AR	Metabolic
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

1,2 fetuses from same family. Abp-825 harbored two distinct reportable findings assigned to different interpretive categories: a heterozygous likely pathogenic DVL1 variant and a biallelic RPGRIP1L finding composed of one likely pathogenic splice-site variant and one missense VUS.

Overview of the identified genetic findings grouped by major developmental or organ-system association. (A) Genetic diagnoses, including definitive molecular diagnoses, and the pathogenic copy-number finding 21q22.12-q22.3 duplication. (B) Possible monogenic contributors. Genes are mapped to their principal affected systems, including neurologic, cardiac, blood/coagulation, kidney anomalies, skeletal, metabolic, ciliopathies, and multi-system involvement. *CPLANE1* and *RPGRIP1L* are shown in both ciliopathy and multi-system categories because of their broader phenotypic effects.

Pedigrees of families with definitive molecular diagnoses in the euploid early pregnancy loss cohort, grouped according to interpretive category. Previous losses, livebirths, and affected fetuses are shown for each family, and recurrent affected fetuses are integrated into the same pedigree when present.

Supplemental Table S1.

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

1–7 fetuses from same family

Supplemental Table S2.

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
	c.1819delT	CPLANE1_c.1819_R	AAGAACGCCAAAGTGATGCTAT	732
	c.7817T>A	CPLANE1_c.7817_F	TGGGTTTGTAGGAGGAGAGGT	471
	c.7817T>A	CPLANE1_c.7817_R	CATACTTCCTGCTCCTTTTCCT	471
	c.5820+3_5820+6del	CPLANE1_c.5820_F	GCCACACAGCATGGCTATATT	431
	c.5820+3_5820+6del	CPLANE1_c.5820_R	TCTCAAGGCTCATCTGGGAT	431
*DHCR7*	c.452G>A	DHCR7_c.452_F	GTGAAGCAAGTTCCATCCCC	586
	c.452G>A	DHCR7_c.452_R	GCAGAACCAAAGGATGGACTC	586
	c.964-1G>C	DHCR7_c.964-1_F	GCAGAACACGCTCTTGACAG	721
	c.964-1G>C	DHCR7_c.964-1_R	CAGGTAGAAGGCAGGTAGAGTT	721
*RBM8A*	c.-21G>A	RBM8A_ex1_F	TGAAGGGGGCGGAATCTCTA	353
*RBM8A*	c.-21G>A	RBM8A_ex1_R	TGCGTGTTTTTACCGTGCAG	353
*NF1*	c.4537C>T	NF1_ex35_F	TGGTCCTGAGGTCTTTTTGG	560
*NF1*	c.4537C>T	NF1_ex35_R	TGTTGTCTTCACTCCCTGGT	560
F5	c.1601G>A	FV-Leiden_F	TGATGCCCAGTGCTTAACAA	265
F5	c.1601G>A	FV-Leiden_R	TCACACTGGTGCTAAAAAGGA	265
*TSC1*	c.3113_3119del	TSC1_ex23_F	GGCTCTCAGAAAGGCTACTGG	436
*TSC1*	c.3113_3119del	TSC1_ex23_R	CATCCTCCGAATGTGGACAG	436
*VWF*	c.3797C>T	VWF_ex28_F	ACCGGGATCACAATGACCTT	632
*VWF*	c.3797C>T	VWF_ex28_R	GTAGGGCTCAGAAGTGTCCA	632
*SLC6A1*	c.740C>A	SLC6A1_ex8_F	AAATGTGAGCTGGTTGGCTC	432
*SLC6A1*	c.740C>A	SLC6A1_ex8_R	AAACCTGGTCTACAGTGAGGG	432
*DSG2*	c.2315del	DSG2_ex14_F	GCCCACTTGACTCAGATCCT	590
*DSG2*	c.2315del	DSG2_ex14_R	TGGGTCCCATTTCTCTTTCCTTA	590
*DVL1*	c.1961dup	DLV1_ex15_F	GGTTGTTCTGGACGTGGC	722
*DVL1*	c.1961dup	DLV1_ex15_R	GGTCTTCCTCATCCCAGGAG	722
*RPGRIP1L*	c.2771G>A	RPGRIP1L_2771G_A_F	GGGGTGGCAGCTTAGTTCTT	389
	c.2771G>A	RPGRIP1L_2771G_A_R	CCTGGCTAGTTCACATGGTAG	389
	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
	c.842C>T	PAH_ex7_R	TCTTTTCATCCCAGCTTGCAC	239
	c.*19G>T	PAH_ex13_F	ACAAGTGGCCCATTTTGATGGT	402
	c.*19G>T	PAH_ex13_R	GGCCCATTTTGATGGTGTTTT	402
*GBA*	c.1444G>T	GBA_ex10_F	CTGCCTCTCCCACATGTGA	391
	c.1444G>T	GBA_ex10_R	CAAAAGGGGATGGGTGTGC	391
	c.1226A>G	GBA_EX9_F	CTTTTCTGCATCGCAGTCCA	459
	c.1226A>G	GBA_EX9_R	TCCCACATGTGACCCTTACC	459
*PKHD1*	c.107C>T	PKHD1_ex3_F	CAGGCCCACTTTTACACCTG	423
	c.107C>T	PKHD1_ex3_R	GGGGCTTCTGATGATGTGTTT	423
	c.10883C>T	PKHD1_ex61_F	ATCAGCCCTCATTTGGATGTGA	537
	c.10883C>T	PKHD1_ex61_R	TTCCATTCACTTGGCCCTCA	537
*PRDM6*	c.1057G>A	PRDM6_ex5_F	ATTGGTTGCTGGGGACAATC	380
*PRDM6*	c.1057G>A	PRDM6_ex5_R	AGTGAACCACGTTTCATGAGT	380
*TBX18*	c.1570C>T	TBX18_ex8_F	GCAACTGGATGAAACAGGGG	1074
*TBX18*	c.1570C>T	TBX18_ex8_R	CTCCAACCCTTGCCTTGTAAC	1074
*SCN5A*	c.3911C>T	SCN5A_ex22_F	CACGGCCATAGGACATCAGA	268
*SCN5A*	c.3911C>T	SCN5A_ex22_R	TGTTCCCATCCTCCCCATTT	268
*MYH3*	c.3137G>A	MYH3_ex25_F	TCTTCTGAAACTGGAGGCCC	345
*MYH3*	c.3137G>A	MYH3_ex25_R	CTTGCAAAGCATTTGTTCCCA	345

Supplemental Table S3.

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

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DOI: https://doi.org/10.2478/bjmg-2025-00028 | Journal eISSN: 2199-5761 (formerly 1311-0160) | Journal ISSN: 1311-0160

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Language: English

Page range: 5 - 20

Published on: May 14, 2026

Published by: Macedonian Academy of Sciences and Arts

In partnership with: Paradigm Publishing Services

Keywords:

early pregnancy loss (EPL),

product of conception (POC),

whole-exome sequencing (WES),

monogenic disease,

euploid early pregnancy loss,

genetic diagnosis

Related subjects:

Medicine,

Basic medical science,

Basic medical science, other

© 2026 Gj Bozhinovski, P Noveski, M Terzikj, K Kubelka-Sabit, D Plaseska-Karanfilska, published by Macedonian Academy of Sciences and Arts
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Volume 28 (2025): Issue 2 (December 2025)

Monogenic Findings in Early Pregnancy Loss: Whole-Exome Sequencing Study of Euploid Products of Conception

Figures & Tables

Figure 1.

Table 1.

Table 2.

Figure 2.

Figure 3.

Supplemental Table S1.

Supplemental Table S2.

Supplemental Table S3.

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