CN-122012688-A - Probe composition, gene chip, reagent, kit and application

Abstract

The invention provides a probe composition, a gene chip, a reagent, a kit and application. The probe composition is designed based on the capture area of 34 genes related to dominant single-gene genetic diseases, can be used for noninvasive prenatal genetics screening, and is suitable for prenatal screening of genetic variation positive family history, bad fertility history, fetal ultrasonic examination abnormality, pregnant woman senior father senior and the like, and the omission rate and birth rate of fetuses suffering from the dominant single-gene genetic diseases are effectively reduced.

Inventors

• WU LINGQIAN
• LI ZHUO
• LIANG DESHENG

Assignees

• 中南大学

Dates

Publication Date

20260512

Application Date

20260109

Priority Date

20250110

Claims (10)

1. 1. A probe composition for detecting dominant monogenic genetic disease, characterized in that the probe composition is designed according to one or more of 34 target genes, the chromosomal location and interval length of the 34 target genes are as follows: 。
2. 2. The probe composition according to claim 1, the dominant monogenic genetic disorder includes Bainbridge-Ropers syndrome, coffin-Siris syndrome type 1, development retardation with variable mental disorder and behavioral abnormality, helsmoortel-van der Aa syndrome, development epileptic encephalopathy type 94, CHARGE syndrome, development epileptic encephalopathy type 27, autosomal dominant inherited mental disorder type 6, with or without epilepsy, white-Sutton syndrome, development epileptic encephalopathy type 4, mowat-Wilson syndrome, development epileptic encephalopathy type 6B, dravet syndrome, familial hemiplegic migraine type 3, kabuki syndrome type 1, kleefstra syndrome type 2, cornelia de Lange syndrome, congenital variation type Rett syndrome, tuberous sclerosis type 94, tuberous sclerosis type 2, autosomal dominant inherited mental disorder type 7, intellectual dominant inherited mental disorder type 43, neonatal severe epileptic encephalopathy, rett syndrome, autosomal dominant inherited disorder type 5, ruin-Len syndrome type 4, mowat-Wilson syndrome, development epileptic encephalopathy type 6B, drave syndrome, familial hemiplegia type 3, kabuki syndrome type 2, kleefstra syndrome type 2, cornelia de Lange syndrome, congenital variation type 4, tacran syndrome type 3, open type 2 syndrome, ehlers-Danlos syndrome type 1 combined osteogenesis imperfecta, ehlers-Danlos syndrome VIIA, osteogenesis imperfecta I-III, osteogenesis imperfecta IV, ehlers-Danlos syndrome type 2 combined osteogenesis imperfecta, ehlers-Danlos syndrome VIIB, ehlers-Danlos syndrome heart valve type, osteogenesis imperfecta II-III, early onset infant epileptic encephalopathy type 2, at least one of agamogenitalia or dyssteroidogenesis Antley-Bixler syndrome, apert syndrome, beare Stevenson cutaneous convolution syndrome, campylodysplasia syndrome, craniofacial skeletal cutaneous dysplasia, crouzon syndrome, jackson-Weiss syndrome, LADD syndrome, pfeiffer syndrome, saethre-Chotzen syndrome, achondroplasia, CATSHL syndrome, crouzon syndrome with acanthosis nigricans, chondrodysplasia, LAD syndrome, muenke syndrome, SADDAN, and lethal dysplasia type I-II.
3. 3. The probe composition of claim 1, wherein the types of probes in the probe composition include conventional probes and InDels mutant probes, the conventional probes comprising one or more probes designed based on a reference sequence of any one of the 34 target genes; the InDels mutant probes include one or more probes designed based on the mutant sequence of any one of the 34 genes of interest.
4. 4. The probe composition of claim 1, wherein the probe composition comprises one or more probes for detecting each of the 34 genes.
5. 5. A gene chip comprising the probe composition according to any one of claims 1 to 4, wherein the gene chip is used for detecting dominant single-gene genetic disease, or the use of the probe composition according to any one of claims 1 to 4 for preparing a gene chip for detecting dominant single-gene genetic disease.
6. 6. A reagent comprising the probe composition according to any one of claims 1 to 4 for detecting a dominant single-gene genetic disease, or the use of the probe composition according to any one of claims 1 to 4 for preparing a reagent for detecting a dominant single-gene genetic disease.
7. 7. A kit comprising a probe composition according to any one of claims 1 to 4 or a gene chip according to claim 5 or a reagent according to claim 6, wherein the kit is used for detecting dominant monogenic genetic disorders.
8. 8. Use of a probe composition according to any one of claims 1-4 or a gene chip according to claim 5 or a reagent according to claim 6 or a kit according to claim 7 in NIPT-MD banking.
9. 9. Use according to claim 8, characterized in that the NIPT-MD pooling is performed by targeted capture of the target gene of the sample to be tested using a probe composition according to any one of claims 1-4 or a gene chip according to claim 5 or a reagent according to claim 6 or a kit according to claim 7.
10. 10. The use of claim 8, wherein the sample to be tested comprises plasma or cfDNA, the lower limit of detection of plasma is 2mL, and the lower limit of detection of cfDNA is 4 ng.

Description

Probe composition, gene chip, reagent, kit and application Technical Field The invention relates to the technical field of medical diagnosis, in particular to a probe composition, a gene chip, a reagent, a kit and application. Background About 3% -5% of newborns in the whole world have functional or structural abnormality of the body at birth, namely birth defects. The causes of birth defects are numerous, and relate to genetic factors, environmental factors, maternal factors and the like, wherein the genetic factors are dominant. Common genetic birth defects mainly include chromosomal disorders, genomic disorders, i.e., chromosomal microdeletion microreplication syndrome (Chromosome microdeletion microduplication syndrome, i.e., MMS), and monogenic disorders. Therefore, the genetic detection of birth defects is enhanced, and the accurate screening and diagnosis before pregnancy and birth are developed, which is an important technical means for effectively reducing the birth rate of the infant suffering from birth defects. 20. Fetal DNA (Cell-FREE FETAL DNA, abbreviated cffDNA), i.e., fetal free DNA, derived from apoptotic cells in the outer layer of placental trophoblasts was found in maternal blood circulation in the 90 s of century. Based on this finding, numerous researchers have developed Non-invasive prenatal screening techniques (Non-INVASIVE PRENATAL TESTING, NIPT for short) and NIPT-plus in tandem in combination with high throughput sequencing techniques, which can be used to screen for fetal chromosomal aneuploidies and MMS. Through continuous development and optimization, the clinical performance of the two prenatal genetics screening technologies is fully verified and widely applied in clinic. For NIPT, NIPT-plus screening positive fetus or other fetus with invasive prenatal diagnosis indication, the diagnosis of chromosome disease and MMS can be carried out by combining genetic technologies such as chromosome karyotype analysis, microarray analysis technology (Chromosomal Microarray Analysis, CMA for short), whole genome copy number variation sequencing (Copy number variation sequencing, CNV-seq) and the like. It can be seen that the prenatal screening technical solution for birth defects caused by chromosomal diseases and MMS is basically perfect and mature, so that the emphasis and difficulty in prenatal screening and diagnosis at the present stage are focused on how to prenatally screen birth defects caused by single gene mutation. The single-gene disease has various types, the comprehensive incidence rate can reach 1 percent, and the single-gene disease accounts for 22.3 percent of birth defects and is one of the important reasons for causing the birth defects. Most monogenic diseases are severely fatal, disabling, fool or teratogenic, and nearly 50% of patients develop disease during childhood, even just at birth. Monogenic diseases can be classified into recessive monogenic diseases and dominant monogenic diseases. Dominant monogenic disease accounts for about 60% of severe postpartum monogenic disease with a higher proportion. Unlike the variant genetic trait of recessive monogenic disease, the pathogenic variation of most dominant monogenic disease patients is not inherited from parents, but is derived from a new-onset (de novo) mutation of the gene, i.e., a variation that occurs during gametoplasia of parents or in early fertilized eggs, and the incidence of the new-onset mutation increases with increasing father age. Dominant monogenic disease accounts for 53% of all monogenic diseases, whereas 74% of them are caused by new mutations, so prenatal screening is an important means of controlling such diseases. However, a large proportion of dominant monogenic disease fetuses have no obvious ultrasound abnormalities in early gestation, so that conventional prenatal ultrasound screening or diagnosis of such dominant monogenic disease can suffer from late discovery or missed detection. In order to solve the problems, research teams at home and abroad develop a non-invasive prenatal screening technology aiming at partial dominant monogenic diseases based on free DNA of fetuses and combined with genetic technologies such as second generation sequencing or liquid drop digital polymerase chain reaction, so as to define the cause of abnormal fetuses earlier, such as 'Preseek' technology developed by the Behler medical institute. However, these techniques, which have been reported so far, have focused on dominant monogenic diseases such as dysplasia, mainly caused by prenatal ultrasound. However, for those dominant monogenic fetuses which have no ultrasound abnormalities or only exhibit ultrasound soft index, there is no mature and applicable prenatal screening technique, such as fetuses with neuro-developmental disorder (Neurodevelopmental disorders, NDDs for short) caused by dominant gene mutation, including common Rett syndrome caused by MECP2, kabuki syndrome caused by KMT2D, etc. In view of