Whole exome sequencing as the first-tier test for patients in neonatal intensive care unit: A Chinese single-center study

doi:10.21203/rs.3.rs-3598324/v1

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Whole exome sequencing as the first-tier test for patients in neonatal intensive care unit: A Chinese single-center study

https://doi.org/10.21203/rs.3.rs-3598324/v1

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Background: Genetic disorders are the part of critical patients in neonatal intensive care unit, it is difficult to establish the diagnosis of pathogenesis via rountine detections and accessory examination. Whole exome sequencing may provide the evidence based on molecular diagnose for genetic disorders. Our aim was to explore the significance of whole exome sequencing for patients in neonatal intensive care unit by the retrospective observational study in a Chinese cohort of neonates.

Methods: The neonatal patients were collected in Tianjin Children’s Hospital from January 2018 to April 2021, who had an acute illness and were suspected with genetic disorders performed by whole exome sequencing. We analysed retrospectively the clinical data, genetic findings, and the relationship between phenotype and genetic variation in this study.

Results: A total of 121 neonates were enrolled in this study. Multiple organ or system were involved in the current study, mainly in metabolic, neurologic, endocrine system. The overall positive rate of whole exome sequencing was 55.4% (67/121), 94 pathogenic or likely pathogenic genomic variants of were identified in 67 neonates, of which the number of copy number varation and single-nucleotide variant were 20 and 74 respectively. The most common inheritance pattern of them was autosomal recessive, up to the rate of 56.7% (38/67), the second one was autosomal dominant inheritance, accounting for 29.8% (19/67). Up to 40 diseases were diagnosed via whole exome sequencing in this study.

Conclusion: Based on the study and the available evidence of this cohort , we strongly recommend and support whole exome sequencing as the first-tier test for patients with suspected genetic disorders in neonatal intensive care unit. Whole exome sequencing demonstrates clinical utility and the significance for patients and their familes in situation of the absence of dignosis.

Genetic disorders

Neonatal intensive care unit

Neonates

Whole exome sequencing

Genetic disorders (GD) are the part of critical patients in neonatal intensive care unit (NICU), accounting for about percent twenty of all infant or neonates deaths [1, 2]. The number of patients diagnosed with GD are more and more increasing in recent years, because the knowledge of GD has gradually increased with the application of genomic sequencing [1, 3]. GD are various and serious in clinic, influencing the diagnosis of patients and the quality of life in their life. It is important for the patients with GD to diagnose timely, which are benefit for the treatment and management in clinic. However, clinical manifestation are usually not typical in the early stage, escapically in newborns in NICU not yet appearing fully. Even, the phenotype of GD may be coverd by other clinical symptoms sometimes, which make it difficult to establish the diagnosis of pathogenesis [4]. In spite of many rountine detections and accessory examination are conducted in the process of diagnosis, even including invasive operations and collecting blood sample many times, which bring a lot of pain for patients and increase the burden of economic for the whole family [5]. Nevertheless, it cannot clarify the true pathogenesis. The rapid evolvement of GD may lead to the death and disability when the diagnosis of GD is delayed or absent and measurement of treatments are not chosen timely.

With the development of molecular diagnostic techniques, genetic tests play an more and more important role in the dignosis of GD [2, 6, 7]. Published studies have demonstated the advantsges of genetic tests in clinic. For example, a single-center study in Beijing Children’s Hospital [8] indicated clinical utility of exome sequencing as a first-tier test for pediatric respiratory diseases, the diagnostic yields of exome sequencing for inherited diseases with respiratory symptoms was 34.6%, which shown exome sequencing could rapidly make a molecular diagnosis and direct the intervention of the positive cases in pediatric respiratory medicine. Another prospective study [9] of whole exome sequencing (WES) applied to infants suspected monogenic disorder provided evidence that using WES as a first-line sequencing test for infants can shorten and simplify the process of diagnosis, and WES provided a higher diagnostic yield than standard testing. But there were few articles about the application in NICU in China. Herein, a retrospective observational study was conducted in a Chinese cohort of neonates to explore the significance of WES for patients in NICU.

Recruitment and data collection

We collected the hospitalized 132 neonates from January 2018 to April 2021 in NICU at Tianjin Children’s Hospital in China, who had an acute illness and were suspected with GD, and were conducted by WES. We excluded the 11 cases with definite etiology, incomplete information, repetitive collection. Thus, one hundred and twenty-one cases were enrolled in this study, shown in Fig. 1. This study was approved by the Ethics Committee of Tianjin Children’s Hospital, and informed consent was obtained from the gurdance or parents. We collected the demographic, prenatal, intranatal information and clinical manifastation, physical examination, accessory examination and family history of enrolled patients.

WES and bioinformatic analysis

Genomic DNA was extracted from the peripheral venous blood of the patients and their parents. WES was performed by Kingmed company (Guangzhou, China) and MyGenostics Inc (Beijing, China), with read lengths of 150bp and an average coverage depth of 100-fold in greater than 95% of the target regions, including all coding regions and exon-intron boundaries. Raw data were aligned to the human reference genome hg19 by Burrows-Wheeler Aligner software. Variant annotations were made using OMIM, HGMD, dbSNP, Clinvar, ANNOVAR, and 1,000 genomes databases. Candidate variants were subsequently filtered by Baylor process. Protein function prediction was performed using SIFT and Polyphen2.

Data reanalysis

We reanalysed the outcome of genetic reports to evaluate the relationship between phenotype and genetic variation, and the pathogenicity classification was assessed through the American College of Medical Genetics and Genomics (ACMG) [10], including five grades: pathogenic, likely pathogenic, variant of uncertain significance, likely benign, and benign.

Clinical information of neonates in NICU

A total of 121 neonates were enrolled in this study, contained 66 male infants and 55 female infants. The age of them at the time of enrollment ranged from 1 hour to 28 days. The most infants of this cohort were full term neonates, accounting for 86.8% (105/121), the ratio of preterm and extremely preterm was 12.4% (15/121) and 0.8% (1/121), respectively. The detailed information are shown in Table 1. Multiple organ or system were involved in the current study, mainly in metabolic, neurologic, endocrine system, the rate of which was 24% (29/121), 17.4% (21/121), 12.4% (15/121) respectivelly, shown in Table 1.

Table 1

Clinical characteristics of neonates
Total number of neonates	N = 121
Gender
Male	66 (54.5%)
Female	55 (45.5%)
Gestational age
Post-term(≥ 42weeks)	0 (0.0%)
Term(37−42weeks)	105 (86.8%)
Preterm(28−37weeks)	15 (12.4%)
Extremely preterm(< 28weeks)	1 (0.8%)
Organ system involvement
Resparitory/Pulmonary	4 (3.3%)
Cardiovascular	5 (4.1%)
Gastrointestinal	9 (7.4%)
Neurologic	21(17.4%)
Hematologic	5 (4.1%)
Endocrine	15 (12.4%)
Renal	3 (2.5%)
Immunologic	7 (5.8%)
Metabolic	29 (24.0%)
Musculoskeletal	5 (4.1%)
Dermatologic	4 (3.3%)
Audiologic	4 (3.3%)
Craniofacial	3 (2.5%)
Ophthalmologic	1 ( 0.8%)
Delay with whole development	6 (5.0%)

Variants information of neonates in NICU

The overall positive rate of WES was 55.4% (67/121), 94 pathogenic or likely pathogenic genomic variants were identified in 67 neonates (shown in Table 2), of which the number of copy number varation (CNV) and single-nucleotide variant (SNV) were 20 and 74 respectively. CNV mainly included deletion mutation and duplication mutation, SNV mainly included missense mutation, nonsensen mutation, frame shift mutation and splicing mutaion. There were 16 de novo varations in this cohort, shown in Table 2. Proportion of inheritance patterns are shown in Fig. 2, the most common inheritance pattern of them was autosomal recessive, up to the rate of 56.7% (38/67), the second one was autosomal dominant inheritance, accounting for 29.8% (20/67).

Table 2

Details of genetic findings in 67 neonates of the current cohort
ID	Gene	Gene variant(s)	Reference sequence	Zygosity	Inherited pattern	The source of variation	Variation type	Variation classification
Patient 1	EXT2	c.514C > T/p.(Gln172*)	NM_207122.1	Het	AD	Father	Nonsense variation	P
Patient 2	CYP21A2	c.293−13C > G/ p.? c.1069C > T/p.(Arg357Trp)	NM_000500.7	Het Het	AR AR	Mother Father	Splicing variation Missense variation	P P
Patient 3	UGT1A1	c.1091C > T/p.(Pro364Leu)	NM_000463.2	Het	AD	Father	Missense variation	LP
Patient 4	SMN1	Exon7/8 deletion	NM_000344.3	Homo	AR	Parent	Deletion variation	P
Patient 5	MMACHC	c.80A > G/p.(Gln27Arg) c.81 + 1G > A/p.?	NM_015506.2	Het Het	AR AR	Mother Father	Missense variation Splicing variation	LP LP
Patient 6	STS	Chrxp22.31 del (including STS gene)	-	Hemi	XLR	De novo	Deletion variation	P
Patient 7	ATP6V0A2	c.117 + 5G > T/p.?	NM_012463.3	Homo	AR	Parent	Splicing variation	P
Patient 8	MMACHC	c.80A > G/p.(Gln27Arg) c.217C > T/p.(Arg73*)	NM_015506.2	Het Het	AR AR	Mother Father	Missense variation Nonsense variation	LP P
Patient 9	CLCNKB	whole gene deletion	-	Homo	AR	-	Deletion variation	P
Patient 10	SCN2A	c.781G > A /p.(Val261Met)	NM_021007.2	Het	AD	Father	Missense variation	P
Patient 11	KCNQ2	Chr20q13.33 del 129kb	-	Het	AD	De novo	Deletion variation	P
Patient 12	SPTB	c.3737delA/p.(Lys1246fs)	NM_000347.5	Het	AD	Father	Deletion variation	P
Patient 13	SMN1	Exon7/8 deletion	NM_000344.3	Homo	AR	-	Deletion variation	P
Patient 14	KCNQ2	c.797A > G/p.(Asp266Gly)	NM_172107.2	Het	AD	De novo	Missense variation	P
Patient 15	MMUT	c.1677−1G > C/p.?	NM_000255.3	Homo	AR	Parent	Splicing variation	P
Patient 16	RUNX2	c.539C > A/p.(Ala180Glu)	NM_001024630.3	Het	AD	De novo	Missense variation	P
Patient 17	KCNQ2	c.629G > A/p.(Arg210His)	NM_172107.2	Het	AD	De novo	Missense variation	P
Patient 18	PKHD1	c.2264C > T/p.(Pro755Leu) c.1969C > T/p.(Gln657*)	NM_138694.3	Het Het	AR AR	Mother Father	Missense variation Nonsense variation	LP LP
Patient 19	GJB2	c.35G > A p.(Gly12Asp)	NM_004004.5	Het	AD	Mother	Missense variation	LP
Patient 20	ASS1	c.380G > T/p.(Arg127Leu)	NM_000050.4	Homo	AR	Parent	Missense variation	LP
Patient 21	VPS13B SLC26A4	c.6940 + 1G > T/p.? c.919−2A > G/p.?	NM_017890.4 NM_000441.1	Homo Homo	AR AR	Parent Parent	Splicing variation Splicing variation	P P
Patient 22	-	chr5p15.33p15.2(140413−14769310)dup 14628.897kb chr18q21.31q23(55711883–78005241)del 22293.358kb	-	-	-	-	Duplication variation Deletion variation	P P
Patient 23	SMN1	Exon7/8 deletion	NM_000344.3	Homo	AR	Parent	Deletion variation	P
Patient 24	CYP21A2	c.293−13C > G/p.? Exon1/3/4/6/7 deletion	-	Het Het	AR AR	Mother De novo	Splicing variation Deletion variation	LP P
Patient 25	MMACHC	c.609G > A/p.(Trp203*) c.567dupT/p.(Ile190fs)	NM_015506.2	Het Het	AR AR	Father Mother	Nonsense variation Frame shift variation	P P
Patient 26	ABCA3	c.115C > G/p.(Leu39Val) c.277G > A/p.(Val93Ile)	NM_001089.2	Het Het	AR AR	Father Mother	Missense variation Missense variation	LP VUS
Patient 27	CASK	c.764G > A/p.(Arg255His)	NM_003688.3	Hemi	XLD	De novo	Missense variation	LP
Patient 28	SMN1	Exon7/8 del	NM_000344.3	Homo	AR	Parent	Deletion variation	P
Patient 29	GAA	c.859−2A > T/p.? c.1861T > G/p.(Trp621Gly)	NM_000152.3	Het Het	AR AR	Mother Father	Splicing variation Missense variation	P VUS
Patient 30	ANK1	c.3365delT/p.(Leu1122Arg)	NM_000037.3	Het	AD	Mother	Frame shift variation	P
Patient 31	ZMPSTE24	c.743C > T/p.(Pro248Leu) chr1p34.2(40747005–41013142) del 266kb	NM_005857.4	Het Het	AR AR	Father -	Missense variation Deletion variation	P P
Patient 32	PCCA	c.2002G > A/p.(Gly668Arg)	NM_000282.3	Homo	AR	Parent	Missense variation	P
Patient 33	PCCA	c.2002G > A/p.(Gly668Arg)	NM_000282.3	Homo	AR	Parent	Missense variation	P
Patient 34	ATP7A	c.2383C > T/p.(Arg795*)	NM_000052.6	Homo	XLR	Mother	Nonsense variation	P
Patient 35	FGA	c.104G > A/ p.(Arg35His)	NM_021871.2	Het	-	Mother	Missense variation	LP
Patient 36	-	chr2q37.2q37.3(236403321–242841491)del 6438.170kb chr22q11.21(20920744–21154064) dup 233.320kb chr18q23(74074443–78005241) dup 3930.798kb	-	-	-	-	Deletion variation Duplication variation Duplication variation	P P P
Patient 37	CPS1	c.2339G > A/p.(Arg780His) c.3520C > T/p.(Arg1174*)	NM_001875.4	Het Het	AR AR	Father Mother	Missense variation Nonsense variation	LP P
Patient 38	SPTB	c.4735C > T/p.(Arg1579*)	NM_000347.5	Het	AD	De novo	Nonsense variation	P
Patient 39	PAX2	c.76dupG/p.(Val26fs)	NM_003987.4	Het	AD	De novo	Frame shift variation	P
Patient 40	CYP21A2	c.293−13C > G/p.?	NM_000500.7	Homo	AR	Parent	Splicing variation	P
Patient 41	STXBP1	c.578 + 1G > T/p.?	NM_003165.3	Het	AD	De novo	Splicing variation	P
Patient 42	NF1	c.3044T > C/p.(Leu1015Pro)	NM_000267.3	Het	AD	De novo	Missense variation	P
Patient 43	MMUT	c.2131G > T/p.(Glu711*) c.1889G > A/p.(Gly630Glu)	NM_000255.3	Het Het	AR AR	De novo Father	Nonsense variation Missense variation	P P
Patient 44	SCN2A	c.2657T > C/p.(Leu886Ser)	NM_021007.2	Het	AD	De novo	Missense variation	P
Patient 45	NIPBL	c.5366G > T/p.(Arg1789Leu)	NM_133433.3	Het	AD	De novo	Missense variation	P
Patient 46	KCNQ2	chr20q13.33(62103511–62103877) del 0.4Kb	-	Het	AD	-	Deletion variation	P
Patient 47	TTN	c.89675delA p.(Lys29892fs)	NM_133378.4	Het	AD	-	Frame shift variation	P
Patient 48	WAS	chrXp11.23(48545160–48549563) del 4.4Kb	-	Hemi	XL	Mother	Deletion variation	P
Patient 49	-	chr1q42.13q44(228969151_249224684) dup 20.3Mb chr9p24.3p23(208455_10287179) del 10.1Mb	-	-	-	-	Duplication variation Deletion variation	P P
Patient 50	PTS	c.286G > A/p.(Asp96Asn) c.317C > T/p.(Thr106Met)	NM_000317.2	Het Het	AR AR	Father Mother	Missense variation Missense variation	P P
Patient 51	CYP21A2	c.293−13C > G/p.? Exon1/3 del	NM_000500.7	Het Het	AR AR	Mother -	Splicing variation Deletion variation	P P
Patient 52	MMACHC	c.80A > G/p.(Gln27Arg) c.658_660del/p.(Lys220del)	NM_015506.2	Het Het	AR AR	Father Mother	Missense variation Deletion variation	P P
Patient 53	PLOD1	c.1095C > T/p.(Gly365=)	NM_000302.3	Homo	AR	Parent	Same sense variation	P
Patient 54	VPS13B	c.4213delG/p.(E1405Kfs*4) c.10244C > T/p.(T3415I)	NM_152564 NM_017890	Het Het	AR AR	Mother Father	Frame shift variation Missense variation	LP VUS
Patient 55	IGHMBP2	c.1813C > T/p.(Arg605*) c.905_912 + 84del/p.(Asp302fs)	NM_002180.2	Het Het	AR AR	Mother Father	Nonsense variation Frame shift variation	P P
Patient 56	SLC26A2	c.1020_1022delTGT/p.(V341del) c.800C > T/p.(S267F)	NM_000112	Het Het	AR AR	Mother Father	Deletion variation Missense variation	LP P
Patient 57	KCNQ2	c.941C > G/p.(Ser314Cys)	NM_172107.3	Het	AD	De novo	Missense variation	LP
Patient 58	HADH	c.493C > T/p.(R165*) c.89T > A/p.(V30E)	NM_005327	Het Het	AR AR	Father Mother	Nonsense variation Missense variation	P P
Patient 59	MMACHC	c.315C > G/p.(Y105) c.481C > T/p.(R161)	NM_015506	Het Het	AR AR	Mother Father	Nonsense variation Nonsense variation	P P
Patient 60	MMACHC	c.445_446delTG/p.(Cys149fs*32) c.658_660delAAG/p.(Lys220del)	NM_015506	Het Het	AR AR	Father Mother	Frame shift variation Deletion variation	P P
Patient 61	BCKDHB	c.550delT/p.(Ser184fs) c.508C > G/p.(Arg170Gly)	NM_183050.3	Het Het	AR AR	Mother Father	Frame shift variation Missense variation	P P
Patient 62	-	chr12p13.33(173787_3077219) del2.9 Mb chrXq27.3q28(145751423_155233731) dup 9.5Mb	-	-	-	-	Deletion variation Duplication variation	P P
Patient 63	PAH	c.478C > T/p.(Q160*) c.688G > A/p.(V230I) c.280A > G/p.(I94V)	NM_000277	Het Het Het	AR AR AR	Mother Father Father	Nonsense variation Missense variation Missense variation	P P P
Patient 64	SLC26A4	c.919−2A > G/(p.splicing)	NM_000441	Homo	AR	Parent	Splicing variation	P
Patient 65	PKHD1	c.4274T > G/p.(L1425R) c.2507T > C/p.(V836A)	NM_138694	Het Het	AR AR	Mother Parent	Missense variation Missense variation	LP LP
Patient 66	SLC25A13	c.852_855delTATG/p.M285Pfs*2 IVS4ins6kb	NM_014251	Het Het	AR AR	Father -	Frame shift variation Insert variation	LP LP
Patient 67	CHD7	c.5569delT/p.(Y1857Ifs*12)	NM_017780	Het	AD	De novo	Frame shift variation	P
Abbreviations: AD, autosomal dominant; AR, autosomal recessive; Hemi, hemizygous; Het, heterozygous; Homo, homozygous; LP, likely pathogenic; P, pathogenic; VUS,variant of uncertain significance; XL, X-linked; XLD, X-linked dominant; XLR, X-linked recessive; -, unknown/absent.

Genetic disorders diagnosed by WES

Up to 40 diseases were diagnosed via WES in this study. The top four disorders in this cohort were epilepsy (EP) (9/67, 13.4%), methylmalonic acidemia (MMA) (8/67, 12.0%), spinal muscular atrophy (SMA) (5/67, 7.5%), congenital adrenal hyperplasia (CAH) (4/67, 6.0%), shown in Fig. 3. Furthermore, we also found the top three organ system involved were renal system(3/3, 100%), audiologic system(4/4, 100%), and neurologic system(17/21, 81%) in this cohort.

WES has been recommended as a first-tier clinical diagnostic test for children patients who infected with developmental delay, intellectual disability, and respiratory disease et al [8, 11]. But there were few article about the application in NICU in China. In this study WES was performed for 121 infants with unknown diagnosis in NICU at Tianjin Children’s Hospital of China, with an overall diagnostic yield of 55.4% (67/121), higher than the published study with the rate of 37.9% about exome sequencing in neonates in USA [12]. Among the positive cases, the most frequent indentified diseases were epilepsy and methylmalonic acidemia (MMA), accounting for 13.4% (9/67), 12.0% (8/67 ), respectively.

MMA resulting from methylmalonyl-CoA deficiency or abnormal cobalamin metabolism is a rare inherited metabolic disease, mainly inherited in autosomal recessive mode, and is the most commom organic acidemia [13]. As we all know, there are several kinds of pathogenic gene, including MMACHC, MMADHC, MUT, etc. The spectrum of gene variation varies in different countries and populations [14–16]. In China, the three most frequent variants of MMACHC gene in children with MMA were c.609G > A, c.658_660 delAAG, and c.80A > G, with frequencies of 34.09%, 13.64%, and 13.64%, respectively [14]. In this study, among the 8 MMA cases, we identified 12 mutations of 2 genes (MMACHC, MMUT), including one de novo mutation ( MMUT c.2131G > T/p.Glu711*) and eleven inherited mutations, of which 9 gene mutations of MMACHC were found, 3 gene mutatons in MMUT were identified. A total of 12 MMACHC gene mutations were determined, the frequency of c.658_660 delAAG and c.80A > G was 16.7% (2/12), 25.0% (3/12), respectively, which were consistent with the previous published study in China [14, 15]. Among 8 cases, only one case was homozygous, the other 7 cases were compound heterozygous. There were the same inherited pattern in 8 MMA cases, namely autosomal recessive. To our knowledge, the manifestations of MMA are nonspecific and various in patients, especially in newborn and young infant. Previous study indicated that the clinical course was progressive rapidly in combined MMA neonates, even resulting to death due to lacking of prompt treatment [17]. Furthermore, more than 90 percent cobalamin C patients are serious early onset [18]. Comfortingly, it is a treatable genetic disorders for most patients with MMA [19]. On a case from our team [20], We reported a neonate with MMA metabolic decompensation (severe metabolic acidosis and hyperammonemia (> 1,000 ug/dl)) successfully treated with automatic peripheral arteriovenous exchange transfusion and L-carnitine, and further certified the diagnosis of MMA by WES, which resulted in gradually decreased serum ammonia levels and clinically improved status of the child. Thus, WES detection is crucial to diagnose this disease and can help to treat timely and improve the prognosis for the patients in NICU.

Neonatal seizures is one of the most commom manifestation of neurological dysfunctions, the incidence of which is about 1–5‰ [21, 22]. Although the mortality of neonatal seizures has decreased from 40–20%, the outcome of neurodysplasia has not significantly improved, such as cerebral palsy, mental retardation, secondary epilepsy, etc [22]. Therefore, recongnizing the eitology of neonatal seizures and timely medical therapy is the key to manage the diseases. The reason of neonatal seizures are complex, such as acute symptomatic seizures, electrolyte imbalance and cerebral deformity, and so on [22, 23]. With the advancement of molecular diagnostic technology, the detection rate of neonatal seizures caused by genetic disorders has gradually increased in recent years [24]. At the same time, WES as one of the important molecular diagnostic technology paly an crucial role in identifying the etilogy of neonatal seizures. In this research, 9 positive cases were indentified by WES test, who were admitted to hospital as a result of the onset of seizures during the neonatal period. We found 9 mutations of 4 pathogenic gene associated with the seizures in 9 cases, which contained 6 missense mutaions, 2 deletion mutations and 1 splicing mutation, and also belonged to 3 inherited variations and 6 de novo variations in the sense of the source of variation. For example, in patient 10 (shown in Table 2), we ascertained that the underlying etiology of neonatal seizures was caused by the variotion of SCN2A c.781G > A /p.(Val261Met), and confirmed that the final diagnosis was benign familial neonatal convulsions, which was a kind of benign epilepsy with a good prognosis. Thus, WES test not only was used to indenitfy the genetic etiology but also to provide the precise therapy for patients in NICU.

In patient 29 (shown in Table 2), a female term infant was admitted to NICU of Tianjin Children’s Hospital at the age of 25 days because of jaundice and elevated liver enzymes. This girl was born to a 32 years old woman with normal history of pregnancy and delivery. Physical examination at admission was not abnormal except for jaundice. Laboratory investigations showed elevated creatine kinase and glutamic-pyruvic transaminase. In addition, ultrasonic cardiogram showed left and right ventricular hypertrophy. Therefore the primary diagnosis of this patient were neonatal jaundice, abnormal liver function, suspected hypertrophic cardiomyopathy. Given that the etiology was not clear, she accepted symptomatic treatment and performed WES detection. However, genetic testing showed two heterozygous variants of the GAA gene located on chromosome 17q25 at c.859-2A > T (p.?) and c.1861T > G (p.Trp621Gly), which confirmed the diagnosis of glucogen storage disease type II, namely Pompe disease, considerably different from the primary diagnosis. As is known to all, Pompe disease is a rare autosomal recessive disorder caused by mutations in the GAA gene and is a chronic and progressive pathology usually characterized by limb-girdle muscle weakness and respiratory failure [25]. Early diagnosis is essential to prevent or reduce the irreversible organ damage associated with Pompe disease progression [26]. Nonetheless, the patient in our cohort had no classical clinical phenotype at the time of admission, which became a challenge for clinicians to diagnose timely. Therefore, WES became an important complement for undiagnosed patients with a wide spectrum of clinical phenotypes ranging from isolated hyper-CKemia to mild or severe muscular impairment. This case indicated the significance of WES for patients with suspected genetic disorders in NICU, whose diagnosis were unclear because of widely varing clinical phenotypes.

However, WES analysis yielded negnitive diagnostic rate of 44.6% (54/121) in this cohort, possibly due to the limitation of WES. For instance, although WES could widely detect a variety of variants, there are limited ability to indentify the variants of noncoding region, abnormal genome structure, and genomic methylation [27, 28]. Nevertheless, WES has the advantage and significance in following aspects. At first, the detection range of WES is greatly wide and the price has lowered significantly and become acceptable for most parents. Secondly, WES is valuable on the precision diagnosis and treatment strategy. It may be possible to increase the number of infants in NICU who are diagnosed with GD and decrease infant mortality and morbidity related to GD via early neonatal diagnosis. Finally, the significance of WES is helpful to genetic consultation for couples with GD infants to make meaningful reproductive choices. WES as a powerful complement to routine detections is the essential means of diagnosing GD for patients in NICU.

In conclusion, we found that whole exome sequencing palyed an crucial role not only in identifying the etilogy but also providing the precise therapy and improving the prognosis for the patients suspected genetic disorders in NICU, whose diagnosis were unclear because of widely varing clinical phenotypes. Based on the study and the available evidence of this cohort, we strongly recommend and support WES as the first-tier test for patients with suspected GD in NICU, which will be an irresistible trend in the era of precision medicine. WES demonstrates clinical utility and the significance for patients and their familes in situation of the absence of dignosis.

GD Genetic Disorders

NICU Neonatal Intensive Care Unit

WES Whole Exome Sequencing

CNV Copy Number Varation

SNV Single-Nucleotide Variant

EP Epilepsy

MMA Methylmalonic Acidemia

SMA Spinal Muscular Atrophy

CAH Congenital Adrenal Hyperplasia

Acknowledgments

Not applicable.

Authors’ contributions

All authors contributed to this manuscript. Yang Liu, Chunquan Cai, and Jianbo Shu conceived and supervised the study. Ruiping Zhang conceived the study, analyzed the data, and wrote the manuscript. Xiaoyu Cui, Huiqing Ma, and Jing Gao conducted and analyzed the data. Yan Zhang and Ying Zhang collected and acquired the clinical data. All authors reviewed and approved the final manuscript.

Funding

This work was supported in part by grant 21JCYBJC00370 from Tianjin Municipal Science and Technoly Bureau and grant TJWJ2021ZD007 from the Public Health and Technology Project of Tianjin and grant 21JCZDJC00390 from the Program of Tianjin Science and Technology Plan and grant Y2020003 from Key Project of Tianjin Children’s Hospital and grant 21JCZDJC01030 from Natural Science Foundation of Tianjin. This study was also funded by Tianjin Key Medical Discipline (Specialty) Construction Project (grant number TJYXZDXK-040A).

Availability of data and materials

All data generated or analysed in this study are included in this published article.

Ethics approval and consent to participate

This study was approved by the Ethics Committee of Tianjin Children’s Hospital, and written informed consent was obtained from the gurdance or parents.

Consent for publication

No individual consent for publication is required for this study.

Competing interests

The authors declare no competing interests.

Author details

¹Department of Neonatology, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Beichen District, Tianjin, China. ²Graduate College, Tianjin Medical University, Heping District, Tianjin, China. ³Tianjin Pediatric Research Institute, Tianjin Children’s Hospital/Tianjin University Children’s Hospital, Beichen District, Tianjin, China. ⁴Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Beichen District, Tianjin, China. ⁵The Pediatric Clinical College in Tianjin Medical University, Heping District, Tianjin, China.

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No competing interests reported.

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Whole exome sequencing as the first-tier test for patients in neonatal intensive care unit: A Chinese single-center study

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Abstract

Figures

Background

Methods

Recruitment and data collection

WES and bioinformatic analysis

Data reanalysis

Results

Clinical information of neonates in NICU

Variants information of neonates in NICU

Genetic disorders diagnosed by WES

Discussion

Conclusion

Abbreviations

Declarations

References

Additional Declarations

Status:

Version 1