3 Patterns of Congenital Malformations

A malformation or structural defect of an organ can be an isolated anomaly or may be associated with major or minor anomalies or variants of other systems. Multiple malformations are classified into syndromes, sequence and association. This gives an idea about the etiopathogenesis and is useful in clinical approach to the management.

• Syndrome: A syndrome is often used to describe a pattern of malformations occurring together and definitely or presumably caused by a common etiology. The syndrome may be due to a chromosomal etiology (e. g. Down syndrome due to trisomy 21), a microdeletion syndrome (e. g. Williams syndrome due to a submicroscopic deletion on chromosome 7q11), or mutation in a gene (eg. Apert syndrome due to mutation in FGFR2 gene).
• Sequence: A single malformation may lead to a chain of events leading to multiple anomalies and such a group of anomalies is known as sequence. An example is congenital absence of kidneys leading to oligohydramnios; which in turn leads to flattening of face, lung hypoplasia and clubfeet, called the Potter sequence.
• Association: The co-occurrence of a group of malformations together more frequently than can occur by chance, without an identified common etiology, is labelled as an association. As genomic techniques are identifying etiologies, some of the cases previously described as associations are being regrouped as syndromes. E.g. some cases of CHARGE (Coloboma, Heart defect, Atresia choanae, Retarded growth, Genital and Ear anomalies) association are now found to be due to mutation in the CHD7 gene.

4 Clinical Presentation of Malformations

Many malformations such as neural tube defects manifest at birth either because they are obvious on external examination or may present with symptoms due to the resulting functional defect e.g. tracheoesophageal fistula. Some internal anomalies like atrial septal defect, hydronephrosis due to pelviureteric junction obstruction or ectopic kidney may go undetected for many years. Nowadays, many major malformations are getting detected prenatally due to routine antenatal ultrasonographic evaluation. Some fetuses with malformation(s) may get spontaneously aborted or are stillborn. A neonate with a major malformation is an emergency and evaluation for associated major or minor malformations for making an etiological diagnosis is essential in addition to supportive care and appropriate curative surgery.

5 Importance of Etiological Diagnosis of Congenital Birth Defects

Most of the congenital birth defects are genetic in origin; though in some cases the definite genetic defect is not still identified. Other causes are teratogens. For some malformations, especially isolated malformations like neural tube defects and pyloric stenosis, multifactorial etiologies encompassing multiple genetic variations interacting with environmental factors like folic acid intake are hypothesized. One type of congenital malformation may be caused by different etiologies and the etiological diagnosis can be made by evaluating for associated features and genetic tests. Table 2 shows one example where the enlargement of lateral ventricles in brain can be due to various causes and risk of recurrence depends on the etiology. Figure 2 shows brain imaging showing dilatation of ventricles of the brain due to different etiologies.

As seen in Table 2, risk of recurrence of the malformation and the prognosis varies depending on the etiology. Etiological diagnosis also helps in early detection of treatable complications by surveillance and in assessing the risk of recurrence in subsequent offspring in the family.

6 Clinical Approach to a Patient with Congenital Malformation(s)

A patient, usually a child or a neonate is brought for evaluation due to presence of a major malformation or due to presence of multiple anomalies (often it may be just different looking facial features or facial dysmorphism) which may or may not be associated with developmental delay/ intellectual disability or other neuro-developmental disorders like autism. The clinician should evaluate for associated major malformations, functional disabilities like developmental delay or deafness and most importantly attempt to identify the etiology. The process of diagnosis may be long drawn in many cases. The clinician needs to take into account the understanding and expectations of the parents, their psychosocial and educational background and talk to the family with empathy, so that the family is convinced about the desire of the clinician to help the patient. Good communication with the patient and family helps to give them confidence and get their co-operation and commitment which are needed for the evaluation, which often involves a series of tests, some of which may not give any diagnostic results. Children with dysmorphic features and their parents may be sensitive to the ‘different’ looks and affected individuals often have a poor body image. The dysmorphic features are of diagnostic importance and need to be noted by careful examination of the affected child and sometimes parents also. However, during the clinical examination, utmost care should be taken not to hurt the family by using unfriendly/ insensitive descriptive terms. Photographic documentation is important but should be done only after written consent of the patient or the parents.

7 Clinical Evaluation

The clinical approach to a child with malformation or dysmorphism includes detailed clinical history and thorough head-to-toe and systemic examination. The prenatal history and family history play very important roles (Table 3).

8 Examination of a dysmorphic child

The initial part of evaluation is anthropometric measurement of the height / length, weight and head circumference and comparison with age/sex matched controls. The head-to-toe examination should be carried out by careful evaluation after removing clothes. Facial dysmorphism, hair pattern, nails, neck, fingers and toes, body hair, and pigmentary abnormalities need to be noted. Some features may be present in either of the parents and suggest that the feature is a familial character and may not be related to the etiology of developmental delay / intellectual disability or a syndrome. The American Journal of Medical Genetics had published a special issue on the definitions and descriptions of various human phenotypic variations and this issue is freely available online http://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.v149a:1/issuetoc. A standardized vocabulary for phenotypic variations has been developed and is known as the Human Phenotype Ontology (HPO). At present there are more than 11000 terms. The uniformity of nomenclature helps in clinical diagnostics based on clinical features (Phenomyzer - http://compbio.charite.de/phenomizer/) and also research on relationships between clinical phenotyping and molecular, cellular and biochemical abnormalities and pathways.

9 Search for syndromic diagnosis

Once the clinical assessment of phenotypic variations is done, the next step is to search for the etiological diagnosis or syndrome. There are two processes for the diagnosis of a syndrome. There are some syndromes with characteristic phenotypes and especially the common syndromes can be diagnosed based on the typical dysmorphic features (gestalt). The key features, which are diagnostic clues for such syndromes, are known as ‘Pearls of dysmorphology’. Figure 3 shows typical cases of some common syndromes with malformations.

10 Use of Databases for Syndrome Search

More than 5000 multiple malformation syndromes are described in literature and many new ones are getting delineated. It is impossible to remember all the features of each syndrome and to clinically diagnose the rarer conditions, even for a dysmorphology expert. For this purpose, there are databases of multiple malformation syndromes (Table 4) and these can help experts and newcomers in dysmorphology to get differential diagnoses for each case. The phenotypic abnormalities which are used as search handles in any database have to be specific and uncommon. Eg. midline cleft lip, preaxial polydactyly, microphthalmia are good search handles while microcephaly, cleft lip, intellectual disability, short stature, hypertelorism are poor handles as they will give a long list of differential diagnoses.

As medical genetics is a very rapidly advancing specialty, literature search for latest developments should be a part of syndrome diagnosis and genetic counseling.

11 Role of Investigations in Dysmorphology Diagnosis

Investigations have two important roles in the evaluation of a child with dysmorphism. The first is to look for internal anomalies or associated treatable entities and surveillance for complications. Table 5 gives some representative examples. In some cases the presence of internal malformations also provides support to the clinical diagnosis as is the case in Marfan syndrome.

The other important role of investigations in evaluation of a case with dysmorphology is identification or confirmation of etiology.

12 Genetic Tests

Genetic disorders are classified into chromosomal disorders, single gene (also known as Mendelian as they follow Mendel’s laws of inheritance) disorders and multifactorial. There is no confirmatory laboratory investigation for multifactorial disorders but chromosomal abnormalities may need to be ruled out in some malformations before labeling the malformation as multifactorial. Chromosomes have been studied by traditional karyotyping for more than 5 decades (Figure 4). However, now techniques using DNA principle of complementary regions (A to T and G to C) annealing each other are used to study small regions on chromosomes which are beyond the resolution of traditional karyotyping. These molecular cytogenetic techniques are Fluorescence In Situ Hybridization (FISH), Quantitative Fluorescence Polymerase Chain Reaction (QF-PCR), Multiplex Ligation Probe Amplification (MLPA) and Cytogenetic MicroArray (CMA). Table 6 gives principles and appropriate indications of these tests (Figure 5).

The other group of tests is for identifying mutations in genes causing monogenic disorders. Most of the mutations are variations in the DNA sequence and are identified by Sanger sequencing using automated sequencers (Figure 6). Before ordering the test the clinician should have a working diagnosis with a known causative gene. It needs to be noted that the identification of a causative gene confirms the diagnosis; absence of mutation in a suspected gene does not rule out the diagnosis. The causes in such situation can be different like, inability of the technique to detect the type of mutation, mutation in other parts of gene like introns, promoter, etc. which are not usually tested, or the causative gene may be other than the one tested. It has been seen in a number of disorders that different genes may cause a clinically similar phenotype and some of the genes still may not have been identified. The updated information about all known genes and phenotypes is available on Online Mendelian Inheritance in Man (OMIM), a free database.

For most of the Mendelian disorders, hundreds of mutations are identified and to identify the mutation, sequencing of all coding regions (exons) needs to be done. As many genes have 20 or more exons, the process is tedious and costly. The use of Sanger sequencing for diagnosis in clinical settings gets complicated by involvement of multiple genes causing the clinically indistinguishable phenotypes. This problem has been solved by the latest high throughput sequencing technique known as Next Generation Sequencing (NGS). NGS is routinely used in clinical settings to sequence multiple genes in one go (eg., genes in RAS- MAPK pathway which cause clinically overlapping phenotypes like Noonan syndrome, Cardio-facio-cutaneous syndrome, Costello syndrome, etc). It is also useful for sequencing large genes like the FBN1 gene which causes Marfan syndrome. NGS based sequencing of coding regions (exons) of all genes known as Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) is used in cases where identification of the candidate gene based on phenotype is not possible as the phenotype is novel or subtle. This helps in identification of the causative mutation in 30 to 50% of cases with developmental disorders and causative genes for many novel phenotypes are getting identified. As is the case in CMA, WES identifies thousands of variations in each individual and most of them are polymorphic and non-pathogenic. Dissecting the results of WES to identify the causative pathogenic mutation is a challenging task which needs high level of computational expertise, bioinformatic tools along with clinical correlation and functional studies of the variation. NGS based mutation detection in cases with malformation with or without developmental disabilities helps to identify new mutations and sometimes new genes, and also widens the phenotypic spectrum by identifying a mutation in a known gene which was not suspected on the basis of the clinical phenotype.

13 Genetic Counseling and Prenatal Diagnosis

Congenital malformations are heterogeneous and as a group, a common entity. Counseling regarding prognosis, treatment options, and outcome with surgical and non-surgical interventions is important in prenatally as well as postnatally detected malformations. Genetic counseling about the risk of recurrence and prevention by prenatal diagnosis during the next pregnancy is an important part of management of a family with a child or a pregnancy with birth defect. Accurate genetic counseling needs correct etiological diagnosis of the proband (child or fetus with birth defect). Careful ultrasonographic evaluation of fetus at 18 to 20 weeks can prenatally detect most of the major malformations. Fetal autopsy has a major role in the evaluation of stillbirths and fetuses terminated after prenatal diagnosis of a malformation.

14 Conclusion

Evaluation of an individual with dysmorphism needs expertise and knowledge about syndromes, basic genetics and principles of genetic investigations and their interpretation. Etiological diagnosis helps in appropriate management of the affected individual as well as in accurate genetic counseling of the family.