Human Genetics Methods: Pedigree, Twin Study, Karyotype, Biochemical and DNA Technology

9.1 Human Genetics – Methods and Application: Methods for study of genetic principles in man-family study (pedigree analysis, twin study, foster child, co-twin method, cytogenetic method, chromosomal and karyo-type analysis), biochemical methods, immunological methods, D.N.A technology and recombinant technologies

Official Syllabus: Paper I, Unit 9.1

Unit 1.7 explained the cell, DNA, genes, mutation and chromosomes: in short, genes are stretches of DNA carried on 46 chromosomes, copied at each cell division and passed half from each parent. This unit asks a different question: how do we find out whether, and how, a human trait is inherited? Mendel’s laws as applied to man are in Unit 9.2, gene frequencies in Unit 9.3, and chromosomal disorders in Unit 9.4.

1. Why Human Genetics Needs Special Methods

In Gadchiroli district of Maharashtra, sickle-cell screening up to July 2026 tested about 4.9 lakh people and found about 24,000 carriers and 2,654 patients (Ministry of Health and Family Welfare). To tell a family whether a child will inherit the disease, a geneticist must know how the trait passes from parents to children. Breeding experiments are impossible; the answer has to come from families that already exist and from tests on blood and DNA.

1.1 The obstacles

• No controlled matings: a geneticist cannot choose who marries whom.
• Small families (too few children for reliable ratios) and long generations (25–30 years).
• Heterozygosity: most people carry two different versions (alleles) of many genes, so pure lines do not exist.
• Uncontrolled environment: diet, disease and culture vary between homes, blurring the effect of genes; and ethics forbid experimental exposure.

1.2 The solution: “experiments of nature” and the laboratory

Since experiments cannot be made, geneticists use situations that nature and society have already created, and laboratory methods that read the genetic material directly. The table matches each method to the question it answers; the rest of the unit explains each.

Method	Question it answers	Key idea
Family study, pedigree	Is the trait inherited, and in which pattern?	Trace the trait through relatives
Twin study	How much of the variation is genetic?	Compare identical with fraternal twins
Foster child (adoption)	Genes or home environment?	Compare adoptees with biological and adoptive parents
Co-twin control	What does one factor do, genes held equal?	Treat one identical twin; use the other as control
Cytogenetic, karyotype	Is a chromosome missing, extra or broken?	Stain and arrange chromosomes
Biochemical	Which protein or enzyme is faulty?	Measure gene products
Immunological	Which antigens does a person carry?	Antigen–antibody reactions
DNA and recombinant	What is the exact DNA difference?	Cut, copy, read and transfer DNA

The first four are statistical, whole-person methods that infer genes from resemblance among relatives; the last four are laboratory methods that read the genes or their products. The history of human genetics is a move from the first group to the second, but the family methods remain the starting point in every clinic.

• Heredity and environment: the English polymath Francis Galton (cousin of Darwin) coined the pairing “nature and nurture” (1874). Every method in this unit tries to separate the two, yet most traits depend on both and on their interaction (G × E): a tall genotype grows tall only with enough food.
• Variation within and between groups: the American geneticist Richard Lewontin (1972) found that about 85 per cent of human genetic variation lies within populations and only a small share between so-called races. This is the basis of the view that genetic similarities far outweigh racial differences (Unit 9.5).

2. Family Study and Pedigree Analysis

2.1 Family study

A family study compares how often a trait appears among relatives of affected persons with how often it appears in the general population. Relatives share genes in known proportions (a parent and child share half: the coefficient of relationship is ½), so familial clustering that rises with closeness of kinship suggests a genetic cause.

• Galton‘s Hereditary Genius (1869) traced eminence through families, confusing inherited ability with inherited advantage.
• The English physician Archibald Garrod (1902) noticed that alkaptonuria (urine turning black) appeared in brothers and sisters whose parents were often first cousins: the first human trait shown to follow Mendelian recessive inheritance.
• Limit: families share homes as well as genes, so clustering alone cannot separate heredity from environment; twin and adoption studies are needed for that.

2.2 Pedigree symbols

A pedigree is a chart of a family showing the transmission of a trait across generations. Standard symbols were set out by the American National Society of Genetic Counselors (Bennett and colleagues, 1995; revised 2008 and 2022):

• Square male, circle female, diamond sex unknown; filled symbol = affected; half-filled or central dot = carrier.
• Horizontal line = mating; double line = consanguineous mating (between relatives); vertical line to a horizontal sibship line = children.
• Diagonal slash = deceased; arrow = proband (the person through whom the family came to notice; propositus if male, proposita if female).
• Twins: two lines from one point; a short bar joining them marks identical twins.
• Roman numerals number generations (I, II, III); Arabic numerals number individuals within a generation (II-3).

2.3 Reading the pattern

The power of a pedigree lies in a few rules. Each pattern leaves a recognisable signature; the table lists them, and the diagram shows three side by side.

Pattern	Signature in the pedigree	Examples
Autosomal dominant	Every affected person has an affected parent; appears in every generation (vertical); both sexes equally; father to son possible; unaffected members do not pass it on	Huntington disease, achondroplasia, brachydactyly, polydactyly
Autosomal recessive	Usually born to unaffected carrier parents; skips generations (horizontal, among siblings); both sexes; consanguinity common	Sickle-cell disease, β-thalassaemia, albinism, phenylketonuria
X-linked recessive	Mostly males; passed through carrier mothers; never father to son; affected men’s daughters are all carriers	Haemophilia (Queen Victoria’s descendants), red-green colour blindness, Duchenne muscular dystrophy, G6PD deficiency
X-linked dominant	Affected father → all daughters, no sons; affected mother → half of all children	Hypophosphataemic (vitamin D-resistant) rickets
Y-linked (holandric)	Father to all sons only	SRY (male determination), some male-infertility genes
Mitochondrial	Mother to all children; never through fathers	Leber hereditary optic neuropathy

The three questions that decide most pedigrees follow from the table: Does it skip generations? (recessive). Are males mostly affected, with no father-to-son transmission? (X-linked recessive). Does it pass from father to son? (rules out X-linkage). Older textbooks also list hairy ear rims and webbed toes as Y-linked; these claims rest on doubtful pedigrees and are not accepted today.

2.4 Uses and limits

• Genetic counselling: a pedigree is the first step in counselling. It identifies the pattern, the carriers and the risk to a future child (§10), and guides who should be tested. India’s sickle-cell mission issues genetic status cards so that carriers can use this information before marriage.
• Proving inheritance: to show that a disorder is inherited and how, a geneticist moves step by step: familial clustering → pedigree pattern → twin concordance (§3) → adoption comparison (§4) → segregation ratios (do 1 in 4 children of carrier parents get it?) → linkage and DNA testing (§8).
• Limits: small families; missing or wrong information (an adoption or non-paternity hidden); incomplete penetrance (a carrier of a dominant gene who shows no sign) and variable expressivity; new mutations; and phenocopies (the same symptoms from a non-genetic cause).
• Pedigree and genealogy: the anthropologist’s genealogical method (Rivers, 1900) records social kinship; the pedigree is its biological use, following a trait (Unit 8b).

3. Twin Study

If one identical twin has schizophrenia, the other has it in roughly 48 per cent of cases; for non-identical twins the figure is about 17 per cent (the American psychologist Irving Gottesman, 1991). Since both kinds of twins share a womb, a home and an age, the much higher concordance of identical twins points to genes. Yet it is not 100 per cent, so genes are not the whole story.

3.1 How twins form

• Monozygotic (MZ, identical) twins: one fertilised egg splits into two embryos. They carry the same genes and are always of the same sex. The timing of the split decides the membranes: within about 3 days, two chorions and two amnions (dichorionic diamniotic); days 4–8 (the commonest), one chorion, two amnions (monochorionic diamniotic); days 8–13, one chorion, one amnion (monochorionic monoamniotic); later, conjoined twins.
• Dizygotic (DZ, fraternal) twins: two eggs fertilised by two sperm. They share on average half their genes, like siblings, and may be of different sexes.
• Frequency: MZ twinning is about 3.5–4 per 1,000 births everywhere; DZ twinning varies: about 2 per 1,000 in Japan and China, 6–9 in India and Europe, and about 40 among the Yoruba of Nigeria (the British geneticist Michael Bulmer, The Biology of Twinning in Man, 1970). DZ twinning runs in families on the mother’s side and rises with maternal age; MZ twinning does not.

3.2 History of the method

• Galton (1875, “The History of Twins”) first used twins to weigh nature against nurture, though he did not clearly separate the two kinds.
• The German dermatologist Hermann Werner Siemens (1924) and the American psychologist Curtis Merriman (1924) made the formal comparison of MZ with DZ twins: the classical twin method. Siemens’s “twin rule of pathology”: a heritable condition is more concordant in MZ than in DZ twins.
• The American statistician Karl Holzinger (1929) gave the first heritability index; with Horatio Newman and Frank Freeman he studied 19 pairs of identical twins reared apart (Twins: A Study of Heredity and Environment, 1937).

3.3 Diagnosing zygosity

• Placenta and membranes: a single chorion proves MZ twins; two chorions occur in both kinds, so this test is decisive only one way.
• Similarity method: comparing sex, blood groups and other genetic markers, dermatoglyphics (finger-ridge patterns) and physical traits; any genetic difference proves DZ. Historically, a skin graft accepted between twins indicated MZ.
• DNA markers: today DNA profiling at many short tandem repeat loci (§8.4) settles zygosity with near certainty.

3.4 Concordance and heritability

• Concordant pair: both twins have the trait (or both lack it); discordant: only one has it. For an all-or-none trait (a disease), compare concordance in MZ and DZ pairs; for a measurable trait (height, IQ), compare correlations.
• Pairwise concordance = concordant pairs ÷ all pairs. Probandwise concordance counts each affected twin who brought a pair to notice, and is the proportion of co-twins of affected persons who are also affected; it is the better guide to risk (§10).
• Heritability is the proportion of the variation in a trait, in a given population and environment, that is due to genetic differences. In broad sense (H² = genetic variance ÷ total variance) it includes all gene effects; in narrow sense (h²) only the additive effects that make offspring resemble parents.
• Holzinger’s index: from concordance, H = (C_MZ − C_DZ) ÷ (100 − C_DZ); from within-pair variance, H = (V_DZ − V_MZ) ÷ V_DZ, where V is the variance of the differences between twins of a pair. If genes count for much, MZ pairs differ little (V_MZ small) and H approaches 1.
• Falconer’s formula (the British geneticist Douglas Falconer, 1960): h² = 2(r_MZ − r_DZ), because MZ twins share twice the genetic resemblance of DZ twins. The part of the MZ correlation not explained by genes is the shared family environment (c² = r_MZ − h²).
• Twins reared apart: the Minnesota Study of Twins Reared Apart (the American psychologist Thomas Bouchard and colleagues, Science, 1990) found that MZ twins raised in different homes were nearly as alike in IQ as those raised together, attributing about 70 per cent of IQ variance in that sample to genes.

3.5 Uses and criticism

• Uses: the genetic share of diseases (diabetes, schizophrenia), physical traits (stature: heritability around 0.8 in well-fed populations) and behaviour; and the environmental causes that make identical twins differ.
• Equal environments assumption: the method assumes MZ and DZ twins share environments equally. In fact MZ twins are treated more alike, which may inflate heritability.
• MZ twins are not perfectly identical: they differ through chorion type, placental blood supply, epigenetic marks (chemical tags on DNA that change gene activity) and rare new mutations.
• Heritability is often misread: it refers to a population in a particular environment, not to individuals, and says nothing about differences between groups. A trait can be highly heritable yet strongly changed by environment: average height rose sharply in the twentieth century.

4. Foster Child (Adoption) and Co-Twin Methods

4.1 Foster child (adoption) method

An adopted child receives genes from the biological parents and environment from the adoptive parents. Comparing the child with both separates the two influences more cleanly than family studies, where the same parents supply both.

• Early studies: Frank Freeman, Karl Holzinger and Blythe Mitchell (Chicago, 1928) found foster children’s IQ related to the quality of the foster home; Marie Skodak and Harold Skeels (Iowa, 1949) found adopted children scoring well above their birth mothers, yet still correlated with them: evidence for both environment and heredity.
• Schizophrenia: the American psychiatrist Leonard Heston (1966) followed 47 children of mothers with schizophrenia who had been adopted away at birth: five developed the illness, against none of 50 control adoptees. The Danish adoption studies (Seymour Kety, David Rosenthal and Paul Wender, from 1968) confirmed that risk follows biological, not adoptive, relatives.
• Requirements for a valid study: placement early, before the original home can influence the child; no selective placement (agencies often match children to similar homes, which mixes genes and environment); an adequate sample across social levels; and children from one population, so that ethnic differences do not confound results.
• Limits: prenatal environment comes from the birth mother; adoptive homes are usually better-off than average, narrowing the range of environments; records of birth fathers are often missing.

4.2 Co-twin control method

The co-twin control method uses a pair of identical twins as a natural experiment: one twin receives a training, diet or treatment; the other serves as the control. Since genes, age and home are the same, a difference can be credited to the factor tested.

• Classic study: the American psychologists Arnold Gesell and Helena Thompson (1929) trained one identical infant twin girl to climb stairs for six weeks from the age of 46 weeks; her untrained sister, given just two weeks of training later, soon caught up and climbed faster. Maturation, not early training, set the pace of learning.
• Today: the same logic is applied to discordant MZ pairs in observational data: one twin smokes, the other does not; one was exposed to a disease, the other was not. Any difference in outcome cannot be due to genes or family background.
• Limits: few twin pairs are available; results from a few pairs are hard to generalise; ethical limits on what can be imposed.

Design	What is held constant	What varies	Main weakness
Family study	Nothing cleanly	Degree of kinship	Genes and home mixed
Twin (MZ vs DZ)	Age, womb, home	Genetic similarity (100% vs 50%)	Equal environments assumption
Twins reared apart	Genes (MZ)	Home	Few pairs; similar placements
Adoption	—	Genes from one family, home from another	Selective placement; prenatal environment
Co-twin control	Genes, age, home	One chosen factor	Very small samples

The table shows that each design holds a different thing constant, and each has a different weakness. Conclusions are strongest when several designs agree, as they do for schizophrenia: family, twin and adoption evidence all point to a substantial genetic component.

5. Cytogenetic Methods: Chromosome and Karyotype Analysis

5.1 Milestones

• 1956: Joe Hin Tjio and Albert Levan established the human number as 46 (Unit 1.7).
• 1959: Jérôme Lejeune and colleagues found an extra chromosome 21 in Down syndrome; the same year Charles Ford described 45,X in Turner syndrome and Patricia Jacobs and John Strong 47,XXY in Klinefelter syndrome (Unit 9.4).
• 1960: Peter Nowell found that phytohaemagglutinin (a bean extract) makes lymphocytes divide in culture, and with David Hungerford described the Philadelphia chromosome of chronic myeloid leukaemia, the first chromosome change linked to a cancer. Banding followed in 1970 (Torbjörn Caspersson).

5.2 Preparing a karyotype

1. Sample: usually peripheral blood (lymphocytes); also bone marrow, skin fibroblasts, amniotic fluid or chorionic villi for prenatal diagnosis.
2. Culture about 72 hours with phytohaemagglutinin to stimulate division.
3. Arrest at metaphase with colchicine (or colcemid), which blocks the spindle when chromosomes are most condensed.
4. Hypotonic salt solution swells the cells and spreads the chromosomes; fixation in methanol and acetic acid.
5. Spreading on slides and banding: commonly G-banding (trypsin, then Giemsa stain).
6. Analysis: count at least 15–20 cells (more to detect mosaicism, the presence of two cell lines in one person); photograph; arrange the 22 pairs of autosomes by size and centromere position, then the sex chromosomes.
7. Report in the international shorthand (ISCN): 46,XY (normal male), 47,XX,+21 (female with Down syndrome), 45,X (Turner), 47,XXY (Klinefelter), 46,XX/45,X (a mosaic).

• Banding types: Q (quinacrine, fluorescent; Y chromosome bright), G (Giemsa; dark bands rich in A–T), R (reverse of G), C (constitutive heterochromatin near centromeres).
• An ideogram is a standard diagram of the banded chromosomes, drawn from measurements of many cells; a karyotype is the arranged picture of one cell.

5.3 Molecular cytogenetics

• FISH (fluorescence in situ hybridisation): a fluorescent DNA probe binds to one chromosome region, showing microdeletions too small for the microscope (DiGeorge syndrome, 22q11) or counting chromosomes in non-dividing cells.
• Chromosomal microarray (array CGH): compares a patient’s DNA with a reference across the whole genome, detecting small gains and losses; now the first test for unexplained developmental delay.
• Non-invasive prenatal testing: fragments of fetal DNA in the mother’s blood screen for trisomies without needle sampling.

5.4 Applications

• Diagnosis of numerical and structural aberrations, including sex-chromosome anomalies and their mosaic forms (45,X/46,XX; 46,XY/47,XXY), which are usually milder (Unit 9.4).
• Prenatal diagnosis and reproductive counselling (repeated miscarriage often traces to a parent’s balanced translocation).
• Cancer cytogenetics (Philadelphia chromosome).
• Evolution: humans have 46 chromosomes and the great apes 48; banding shows that human chromosome 2 arose by the fusion of two ape chromosomes.

6. Biochemical Methods

6.1 From inborn errors to molecular disease

• Garrod called alkaptonuria, albinism, cystinuria and pentosuria “inborn errors of metabolism” (Croonian lectures, 1908): each a block in a chemical pathway caused by a recessive gene.
• George Beadle and Edward Tatum (1941), working on bread mould, proposed “one gene, one enzyme”: each step in a pathway is catalysed by an enzyme made under one gene. (It is now “one gene, one polypeptide”, since some proteins are not enzymes and some have several chains.)
• Linus Pauling and colleagues (1949) showed that sickle-cell haemoglobin moves differently in an electric field: sickle-cell anaemia is a “molecular disease”. Vernon Ingram (1956–57) found the cause: one amino acid, glutamic acid replaced by valine at position 6 of the β chain.

6.2 The phenylalanine–tyrosine pathway

One pathway shows how enzyme blocks produce different diseases. Each arrow is an enzyme; a recessive mutation that removes it causes the disorder named.

• Phenylalanine → tyrosine (blocked: phenylketonuria, PKU; phenylalanine builds up and damages the brain unless a low-phenylalanine diet starts early).
• Tyrosine → melanin (blocked: albinism).
• Tyrosine → homogentisic acid → further breakdown (blocked: alkaptonuria, black urine and arthritis; earlier block: tyrosinosis).
• Tyrosine → thyroid hormones (blocked: one form of goitrous cretinism).

6.3 Techniques

• Electrophoresis separates proteins by electric charge (Oliver Smithies‘ starch gel, 1955, revealed many variants); HPLC (high-performance liquid chromatography) is the standard confirmatory test for haemoglobin variants such as HbS; enzyme assays measure one enzyme’s activity (for example G6PD).
• Newborn screening: the American microbiologist Robert Guthrie (1963) devised a test for PKU on a dried blood spot from a heel prick; tandem mass spectrometry now screens one spot for dozens of disorders.

6.4 Applications

• Diagnosis and carrier detection (sickle cell, thalassaemia, Tay-Sachs).
• Newborn screening for treatable conditions: in India, regional programmes (Kerala, Goa, Chandigarh) screen for congenital hypothyroidism, G6PD deficiency, congenital adrenal hyperplasia and others, but there is still no universal national programme.
• Population genetics: frequencies of protein and enzyme polymorphisms (haemoglobin, G6PD, haptoglobin, transferrin) map variation and selection, as in the link between sickle cell, G6PD deficiency and malaria in central India’s tribal belt (Units 9.3 and 9.6).

7. Immunological Methods

• Antigen and antibody: an antigen provokes an immune response; an antibody (immunoglobulin) is the protein made against it. Their reaction can agglutinate (clump) cells, precipitate dissolved antigens or lyse (burst) cells; cell-mediated immunity, by lymphocytes, causes transplant rejection.
• Blood groups: the Austrian-American physician Karl Landsteiner discovered the ABO groups (1901) by mixing serum and red cells: type A people carry anti-B antibodies, type B anti-A, O both and AB neither. Rh followed in 1940 (Landsteiner and Alexander Wiener); an Rh-negative mother carrying an Rh-positive baby can develop antibodies that destroy fetal red cells (haemolytic disease of the newborn).
• First population study: Ludwik and Hanka Hirszfeld (1919) typed soldiers of many nationalities on the Salonika front and found that ABO frequencies varied between populations, founding serological anthropology.
• HLA system: the French immunologist Jean Dausset (1958) found the first human leucocyte antigen; the HLA genes, on chromosome 6, are the most polymorphic in the genome and decide transplant compatibility.
• Techniques: haemagglutination typing; the Coombs test (1945) for antibodies coating red cells; ELISA (1971), which detects antigens or antibodies by a colour change; and monoclonal antibodies (Georges Köhler and César Milstein, 1975), identical antibodies from one cell clone used as precise reagents.
• Applications: safe transfusion and transplantation; prevention of Rh disease (anti-D injection); paternity exclusion before DNA tests (a child with a blood group neither parent could give); disease association (about nine in ten patients with ankylosing spondylitis carry HLA-B27); and population studies of genetic markers: ABO, Rh, HLA and the Gm immunoglobulin types (Unit 9.6).

8. DNA Technology and Recombinant Technologies

In 1988, at the Centre for Cellular and Molecular Biology in Hyderabad, the Indian geneticist Lalji Singh, using a probe developed from a snake (banded krait) DNA sequence, settled a parentage dispute with DNA fingerprinting; in 1991 such evidence was first accepted by an Indian court, in a Kerala paternity case. The Centre for DNA Fingerprinting and Diagnostics followed in Hyderabad (1996). The same tools now serve forensic science, medicine and anthropology.

8.1 The toolkit

• Restriction enzymes: bacterial “molecular scissors” that cut DNA at specific short sequences (Werner Arber, Hamilton Smith and Daniel Nathans; Nobel Prize 1978). DNA ligase is the “glue” that joins fragments.
• Gel electrophoresis separates DNA fragments by size; Southern blotting (Edwin Southern, 1975) transfers them to a membrane where a labelled probe finds one sequence.
• Vectors: plasmids (small circular bacterial DNA) and viruses that carry foreign DNA into a host cell.

8.2 Recombinant DNA technology

Recombinant DNA is DNA joined from two different sources. Stanley Cohen and Herbert Boyer (1973) first inserted foreign DNA into a plasmid and grew it in bacteria.

1. Cut the human gene (for example, for insulin) and the plasmid with the same restriction enzyme, leaving matching “sticky ends”.
2. Join them with ligase to make a recombinant plasmid.
3. Insert it into Escherichia coli; each bacterium copies the plasmid as it divides (gene cloning).
4. Select the bacteria carrying the gene and grow them; they make the human protein.

• Products: human insulin (made in bacteria from 1978; approved for patients in 1982), growth hormone, clotting factors, hepatitis B vaccine, interferons.
• Gene therapy: adding a working gene, or (with CRISPR–Cas9, Jennifer Doudna and Emmanuelle Charpentier, 2012; Nobel Prize 2020) editing a faulty one. Sickle-cell disease was among the first conditions treated by approved gene editing (2023).

8.3 PCR and sequencing

• Polymerase chain reaction (PCR): devised by the American chemist Kary Mullis (1983; Nobel Prize 1993). Each cycle has three steps: denaturation (about 94–96 °C: the two strands separate), annealing (about 50–65 °C: short primers bind on either side of the target) and extension (72 °C: the heat-stable Taq polymerase, from a hot-spring bacterium, copies the strand). Each cycle doubles the target, so 30 cycles give about a billion copies from a single molecule (§10).
• Sequencing: reading the order of bases. Frederick Sanger‘s chain-termination method (1977) uses modified bases that stop copying at A, T, G or C; Allan Maxam and Walter Gilbert (1977) used base-specific chemical cleavage (not restriction enzymes). The Human Genome Project (1990–2003) used Sanger sequencing; next-generation sequencing (from the mid-2000s) reads millions of fragments at once, making whole genomes cheap.

8.4 DNA fingerprinting and profiling

• Invented by the British geneticist Alec Jeffreys (Leicester, 1984) using minisatellites (VNTRs: short sequences repeated a variable number of times), whose band patterns are unique to each person except identical twins.
• Today: PCR-based profiling of short tandem repeats (STRs) at a standard set of loci (20 core loci in the US database) works on tiny or degraded samples.
• Logic of paternity: a child inherits one allele at each locus from each parent. If the child’s paternal allele is absent in the alleged father at several loci, he is excluded; if present at all loci, the probability of paternity is calculated (§10).
• Uses: crime investigation, paternity and immigration disputes, identification of disaster victims, wildlife forensics, and zygosity of twins.

8.5 DNA technology in anthropology and medicine

• Population history: genome-wide data showed that most Indians descend from a mixture of two ancestral groups, “Ancestral North Indians” and “Ancestral South Indians” (David Reich, Kumarasamy Thangaraj, Lalji Singh and colleagues, Nature, 2009); mitochondrial and Y-chromosome DNA trace migrations (Unit 1.7); ancient DNA revealed Neanderthal and Denisovan ancestry (Unit 1.6c).
• Medicine: carrier and prenatal diagnosis (thalassaemia, sickle cell), genome-wide association studies (GWAS: scanning the genomes of thousands of people for variants linked to a disease; Unit 9.4), pharmacogenomics (drug choice by genotype).
• Ethics: privacy of genetic data, informed consent, discrimination, and the misuse of prenatal tests for sex selection, which India’s PCPNDT Act, 1994 (Pre-Conception and Pre-Natal Diagnostic Techniques Act) prohibits.

9. Applications in India

The table links each method to an Indian programme, showing that the syllabus methods are working tools of public policy.

Programme (year)	Methods used	What it does
GenomeIndia (launched 2020; data released January 2025)	Whole-genome sequencing, biobank	10,074 genomes from 83 populations (30 tribal, 53 non-tribal); about 2.7 crore rare variants, 70 lakh not seen in other databases; data at the Indian Biological Data Centre, Faridabad
National Sickle Cell Anaemia Elimination Mission (launched 1 July 2023, Shahdol)	Screening (solubility and point-of-care tests, confirmed by HPLC or electrophoresis), pedigree-based family screening, counselling	Ages 0–40 in 17 states; over 7.26 crore screened, about 2.48 lakh patients and 20.4 lakh carriers found (July 2026); genetic status cards; target of elimination by 2047
UMMID initiative (DBT, 2019)	Biochemical, cytogenetic and molecular diagnosis, counselling	NIDAN Kendras in government hospitals; training clinicians; screening pregnant women and newborns in aspirational districts
Newborn screening (regional)	Biochemical tests on dried blood spots	Congenital hypothyroidism, G6PD deficiency and others in Kerala, Goa, Chandigarh
DNA fingerprinting (CCMB 1988; CDFD 1996)	DNA profiling	Paternity, crime and identification cases

The pattern is that India’s genetic burden is shaped by its social structure: endogamy and consanguinity concentrate recessive disorders in particular communities, which is why GenomeIndia sampled by population group and the sickle-cell mission targets tribal districts.

10. Worked Examples

1. Concordance and Holzinger’s index. In a study, 20 MZ and 20 DZ twin pairs are checked for a disorder; 12 MZ pairs and 4 DZ pairs are concordant.

• C_MZ = 12/20 = 60 per cent; C_DZ = 4/20 = 20 per cent.
• H = (60 − 20) ÷ (100 − 20) = 40/80 = 0.5. Half of the liability is attributed to genes. Discordance is 40 per cent in MZ and 80 per cent in DZ pairs: genetic dissimilarity doubles the chance that twins differ.

2. Holzinger from variances. For a measurement, the within-pair variance is V_DZ = 40 and V_MZ = 10. H = (40 − 10) ÷ 40 = 0.75: three-quarters of the variation is genetic.

3. Falconer’s formula. Twin correlations for a trait are r_MZ = 0.80 and r_DZ = 0.50.

• h² = 2 × (0.80 − 0.50) = 0.60 (genes).
• Shared environment c² = r_MZ − h² = 0.80 − 0.60 = 0.20.
• Unique environment and error e² = 1 − r_MZ = 0.20. Check: 0.60 + 0.20 + 0.20 = 1.

4. Pairwise vs probandwise concordance. Among twin pairs with at least one affected member, 10 pairs are concordant and 20 discordant.

• Pairwise = 10 ÷ 30 = 33 per cent.
• Probandwise = (2 × 10) ÷ (2 × 10 + 20) = 20/40 = 50 per cent: half the co-twins of affected persons are affected.

5. Pedigree risks.

• Autosomal recessive (sickle cell): carrier × carrier (AS × AS) → 1 AA : 2 AS : 1 SS. Risk of an affected child = 1/4 in each pregnancy; an unaffected sibling is a carrier with probability 2/3.
• X-linked recessive (haemophilia): carrier mother × normal father → 1/2 of sons affected, 1/2 of daughters carriers, no affected daughters.
• Autosomal dominant (Huntington): affected heterozygote × normal → 1/2 of children affected.

6. PCR. Starting from one target molecule, copies after n cycles = 2ⁿ. After 10 cycles: 1,024; after 30 cycles: 2³⁰ ≈ 1.07 × 10⁹ (about a billion).

7. A DNA paternity test at three STR loci (numbers are repeat counts):

Locus	Mother	Child	Alleged father	Paternal allele present?
A	12, 14	12, 15	15, 17	Yes (15)
B	8, 9	9, 11	10, 11	Yes (11)
C	6, 7	7, 10	6, 9	No (10 absent)

At locus C the child’s paternal allele (10) is missing from the alleged father. A single mismatch can be a mutation, so laboratories look at many loci; two or more mismatches normally exclude paternity.

Key Terms

Term	Meaning in simple words
Pedigree	A family chart showing who has a trait across generations
Proband	The first family member brought to the geneticist’s notice
Carrier	A person with one copy of a recessive allele, usually healthy
Consanguineous mating	Marriage between blood relatives, such as cousins
Penetrance	How often a gene actually shows its effect in those who carry it
Monozygotic / dizygotic twins	Twins from one egg (identical) / from two eggs (fraternal)
Concordance	Both twins of a pair share the trait
Heritability	The share of differences between people in a population due to genetic differences
Co-twin control	Treating one identical twin and comparing with the other
Selective placement	Adoption agencies matching children to similar homes
Karyotype	A cell’s chromosomes photographed and arranged in pairs
Banding	Staining that gives each chromosome a pattern of stripes
Mosaicism	Two genetically different cell lines in one person
FISH	Using a glowing DNA probe to find one spot on a chromosome
Inborn error of metabolism	An inherited block in the body’s chemistry
Electrophoresis	Separating proteins or DNA in an electric field
HLA	Inherited tissue antigens that decide transplant matching
Restriction enzyme	A protein that cuts DNA at a specific sequence
PCR	A method that copies a piece of DNA millions of times
DNA profiling	Identifying a person from repeat lengths at many DNA spots

Contemporary Developments

• GenomeIndia (2025): the genomes of 10,074 Indians from 83 populations were opened to researchers through the Indian Biological Data Centre in January 2025 and described in Nature Genetics (April 2025); populations are coded numerically, not named, to protect communities (Department of Biotechnology).
• Sickle-cell screening milestone (2026): the mission’s target of 7 crore screenings was reached ahead of schedule; by 26 July 2026 over 7.26 crore people had been screened, about 2.48 lakh patients and 20.4 lakh carriers identified, and 17 Centres of Excellence approved in 15 states (Lok Sabha replies, 31 July 2026).
• Genetic status cards and pre-marital counselling (2026): over 10.49 lakh cards had been distributed in Gujarat’s Valsad district alone, a large-scale use of carrier information in marriage decisions in tribal communities.
• NFHS-6 biomarkers (2026): the survey collected dried blood spots and finger-prick samples for laboratory tests alongside its schedules, showing how biochemical methods now sit inside national household surveys (International Institute for Population Sciences).

Diagrams to Master

1. Topic map: the eight methods, grouped into family-based and laboratory methods.
2. Pedigree patterns: symbols (square, circle, filled, dot, double line, arrow); AD (vertical), AR (horizontal, consanguinity), XR (males, carrier mothers, no father-to-son).
3. Twin method: MZ vs DZ formation; concordance bars; H = (C_MZ − C_DZ)/(100 − C_DZ); h² = 2(r_MZ − r_DZ).
4. Study designs: family, twin, reared apart, adoption, co-twin: held constant / varied / weakness.
5. Karyotype workflow: PHA culture → colchicine → hypotonic → fix → G-band → arrange; ISCN 47,XX,+21.
6. DNA toolkit: cut–join–insert–clone; PCR 94 / 55 / 72 °C, 2ⁿ; STR paternity check.

Revision Grid

Scholar	Work (year)	Key idea
Francis Galton	Hereditary Genius (1869); “The History of Twins” (1875)	Family and twin methods; “nature and nurture”
Karl Landsteiner	1901; Rh 1940 (with Wiener)	ABO and Rh blood groups
Archibald Garrod	1902; Croonian lectures (1908)	Alkaptonuria; inborn errors of metabolism
Hirszfeld and Hirszfeld	1919	Blood groups vary between populations
Siemens; Merriman	1924	Classical MZ–DZ twin method
Gesell and Thompson	1929	Co-twin control: maturation and learning
Karl Holzinger	1929; Twins (1937, with Newman and Freeman)	Heritability index; twins reared apart
Beadle and Tatum	1941	One gene, one enzyme
Linus Pauling; Vernon Ingram	1949; 1956–57	Sickle cell as a molecular disease; Glu → Val
Tjio and Levan	1956	46 chromosomes
Jean Dausset	1958	HLA antigens
Leonard Heston	1966	Adoption study of schizophrenia
Cohen and Boyer	1973	Recombinant DNA
Frederick Sanger	1977	Chain-termination sequencing
Kary Mullis	1983	Polymerase chain reaction
Alec Jeffreys	1984	DNA fingerprinting
Lalji Singh	1988	DNA fingerprinting in India
Bouchard and colleagues	Science (1990)	Minnesota study of twins reared apart