Forensic Science International: Genetics 33 (2018) 10–16

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Forensic Science International: Genetics

journal homepage: www.elsevier.com/locate/fsigen

Research paper

Discrimination of relationships with the same degree of kinship using T

chromosomal sharing patterns estimated from high-density SNPs
⁎
Chie Morimotoa,b, Sho Manabea, Shuntaro Fujimotoa, Yuya Hamanoa,c, Keiji Tamakia,
a
Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
b
Research Fellow of the Japan Society for the Promotion of Science, Japan
c
Forensic Science Laboratory, Kyoto Prefectural Police Headquarters, 85-3, 85-4, Yabunouchi-cho, Kamigyo-ku, Kyoto 602-8550, Japan

A R T I C L E I N F O A B S T R A C T

Keywords: Distinguishing relationships with the same degree of kinship (e.g., uncle–nephew and grandfather–grandson) is
Kinship analysis generally difficult in forensic genetics by using the commonly employed short tandem repeat loci. In this study,
Single nucleotide polymorphisms we developed a new method for discerning such relationships between two individuals by examining the number
Same degree of kinship of chromosomal shared segments estimated from high-density single nucleotide polymorphisms (SNPs).
Chromosomal sharing
We computationally generated second-degree kinships (i.e., uncle–nephew and grandfather–grandson) and
DNA microarray
third-degree kinships (i.e., first cousins and great-grandfather–great-grandson) for 174,254 autosomal SNPs
considering the effect of linkage disequilibrium and recombination for each SNP. We investigated shared
chromosomal segments between two individuals that were estimated based on identity by state regions. We then
counted the number of segments in each pair.
Based on our results, the number of shared chromosomal segments in collateral relationships was larger than
that in lineal relationships with both the second-degree and third-degree kinships. This was probably caused by
differences involving chromosomal transitions and recombination between relationships. As we probabilistically
evaluated the relationships between simulated pairs based on the number of shared segments using logistic
regression, we could determine accurate relationships in > 90% of second-degree relatives and > 70% of third-
degree relatives, using a probability criterion for the relationship ≥0.9. Furthermore, we could judge the true
relationships of actual sample pairs from volunteers, as well as simulated data. Therefore, this method can be
useful for discerning relationships between two individuals with the same degree of kinship.

1. Introduction
In forensic genetics, a pairwise kinship analysis is typically per-
formed to investigate a relationship between two individuals by cal-
culating the likelihood ratio [1]. The likelihood ratio is generally the
ratio between the probability that certain DNA typing results would be
obtained if the pair is related versus that obtained if the pair is un-
related. Meanwhile, when no predicted relationship exists between the
pair (e.g., identification of bone remains, without personal belongings),
all possible relationships should be compared simultaneously. We have
previously proposed a method for pairwise kinship analysis using the
“index of chromosome sharing” (ICS) calculated from high-density
autosomal single nucleotide polymorphisms (SNPs) [2]. In the ICS
calculation, we investigate the genetic length (centi-Morgan (cM)) of all
identity by state (IBS) segments between the two individuals, and then
sum the genetic length of the IBS segments longer than a given
threshold (i.e., 4 cM), which is applied for removing coincidental
matches. Because the ICS values reflect the total genetic length of
shared chromosomal regions between two individuals, the values relate
to the expected proportion of the shared genome (i.e., degree of kin-
ship). Thus, the ICS values in sibling (first-degree relative), un-
cle–nephew (second-degree relative), first cousin (third-degree re-
lative), first cousin once removed (fourth-degree relative), and second
cousin (fifth-degree relative) were distributed as log-normal distribu-
tions, centering around the median values of 2805, 1919, 1018, 544,
and 311, respectively. Using this approach, we could determine the
degrees of kinship up to the third-degree, regardless of sex, even when
the kinship of the pair was totally unpredictable.
However, we probably cannot distinguish relatives with the same
degree of kinship (e.g., uncle–nephew and grandfather–grandson) using
this approach, because these relatives have the same expected total
genetic length of shared chromosomal regions. If possible, adding key
individuals is effective for increasing information [3]. Otherwise, in-
vestigating markers on the sex chromosomes [4–6] might be useful to

⁎
Corresponding author.
E-mail address: ktamaki@fp.med.kyoto-u.ac.jp (K. Tamaki).

https://doi.org/10.1016/j.fsigen.2017.11.010
Received 11 September 2017; Received in revised form 7 November 2017; Accepted 14 November 2017
1872-4973/ © 2017 Elsevier B.V. All rights reserved.
C. Morimoto et al.
discriminate such relationships. For example, Y chromosomal markers
are useful for distinguishing paternal relatives from maternal relatives.
However, it is impossible to discriminate within paternal relationships
such as uncle–nephew and grandfather–grandson. Then, we can theo-
retically distinguish between second-degree relatives by using identity
by descent (IBD) probabilities of two linked loci [7–9]. However, these
studies were not verified by practical data, and the accuracy is un-
known.
Chromosomal sharing patterns, including the number and the ge-
netic length of the actual shared segments (i.e., IBD regions) on the
chromosomes, are expected to differ between relatives, even for the
same degree of kinship, due to differences in the frequency of meioses
and chromosomal transitions from their common ancestors [10–14]. If
two individuals have a collateral relationship, the shared chromosomal
segments are expected to be larger in number and shorter in genetic
length than those in lineal relationship with the same degree of kinship.
This is because the number of recombination events from the common
ancestors is larger in a collateral relationship than that in a lineal re-
lationship with the same degree of kinship [11,13].
In this study, we further developed our previous approach to dis-
tinguish between relationships with the same degree of kinship by in-
vestigating the differences between chromosomal sharing patterns. We
targeted the second and third-degree of kinship, including collateral
and lineal relationships: uncle–nephew vs. grandfather–grandson as
second-degree kinships, and first cousins vs. great-grandfather–great-
grandson as third-degree kinships. We focused on the number of shared
chromosomal segments between two individuals. The shared segments
were estimated on the basis of IBS regions, the effect of coincidental
matches being minimized. For a probabilistic prediction of the re-
lationships between two individuals, we proposed a logistic regression
model, using computationally generated genotypes. We also confirmed
the validity of the proposed method employing actual samples that
were genotyped using DNA microarray.
2. Methods
2.1. Generating computer-based familial genotypes of high-density SNPs
We utilized 249 computationally synthesized familial genotypes
(Fig. 1) of 174,254 autosomal SNPs on the HumanCore BeadChip (Il-
lumina, San Diego, CA, USA) used in our previous study [2].
The SNP haplotypes of the founders (i.e., Nos. 1, 2, 3, 6, 7, and 10 in
Fig. 1) were estimated using the Shape-IT algorithm [15] and 1498
Japanese individuals in the Nagahama Prospective Genome Cohort
[16], to incorporate linkage disequilibrium into the computational
genotypes. We assumed that the founders were unrelated (i.e., non-
inbred pedigrees). We then generated the haplotypes of the descendants
by taking into account recombination events between each SNP based
on sex-averaged recombination rates [17]. The family included two
Fig. 1. Family tree of a family comprising 12 individuals.
11
Forensic Science International: Genetics 33 (2018) 10–16
types of second-degree relative pairs: uncle–nephew (Nos. 5–8 in Fig. 1)
as a collateral relationship, and grandfather–grandson (Nos. 1–8 in
Fig. 1) as a lineal relationship. It also included two types of third-degree
relative pairs: first cousins (Nos. 8–9 in Fig. 1) as a collateral re-
lationship, and great-grandfather–great-grandson (Nos. 1–11 in Fig. 1)
as a lineal relationship.
In the SNP typing system based on DNA microarrays, uncalled
events (i.e., genotypes that cannot be obtained) or genotyping errors
(e.g., a true genotype, AB, is miscalled as AA) occur infrequently even
in pristine DNA samples. In this study, we also included uncalled events
and genotyping errors into the simulated genotypes for each prob-
ability. The values of the two probabilities were determined from the
actual genotyping results of 67 pristine DNA samples typed on the
HumanCore BeadChip (Illumina) in our previous study [2]. Detailed
methods are presented in the Supplementary information and Supple-
mentary Table 1. Uncalled events were randomly generated at all SNPs,
with a probability of 5.97 × 10−4. We assumed that genotyping errors
occurred only in heterozygous genotypes through allele imbalance (i.e.,
one allele in the heterozygous genotype is undetected). Therefore,
genotyping errors were introduced by converting heterozygous geno-
types into randomly chosen homozygous genotypes, with a probability
of 2.28 × 10−4. All programs used for simulations were run using the
statistical software R, version 3.3.2 [18].
2.2. Analyzing chromosomal sharing patterns between individual pairs
We investigated the differences in chromosomal sharing patterns
between collateral relatives and lineal relatives with the same degree of
kinship. We ordered all 174,254 SNPs according to their chromosomal
positions and then counted the IBS state at each locus between two
individuals. The IBS state has three possible outcomes: 0, 1, or 2. SNPs
with uncalled events in either individual are ignored in the subsequent
analysis. We then chose IBS regions (i.e., regions where 1 or 2 are
continuously aligned), which could reflect chromosomal sharing.
However, some IBS regions include coincidental matches, because even
unrelated pairs can share SNPs by chance. Therefore, we have to ex-
clude comparatively shorter IBS regions to minimize the effect of co-
incidental matches. We set a threshold for the genetic length of IBS
regions between two individuals using receiver operating characteristic
curve analysis. We identified IBS regions longer than the threshold (i.e.,
4 cM) as apparent “shared segments.”
To analyze the total amounts of chromosomal sharing, ICS values in
each pair were calculated by summing the genetic length of the shared
segments in the same way as our previous study [2]. In this study, we
also counted the number of the shared segments in each relationship.
We then compared the ICS values and the number of shared segments
between collateral relatives and lineal relatives with the same degree of
kinship: uncle–nephew vs. grandfather–grandson and first cousins vs.
great-grandfather–great-grandson.
2.3. Logistic regression analysis
We used a binary logistic regression analysis to determine whether
the relationship of the pair is collateral or lineal because we assumed
two outcomes (collateral or lineal). We modeled the probability that the
pair has a collateral relationship as a function of the number of shared
segments, using the following equation:
1
Pr(C|x ) =
1 + exp(β0 + β1 x ) (1)
where Pr(C|x ) is the probability that the relationship of the pair is
collateral, and x is the number of shared segments. In this model, β0 and
β1 are the logistic parameters. We estimated β0 and β1 for each degree of
kinship. Pr(L|x ) , the probability that the relationship of the pair is
lineal, can be calculated by Pr(L|x ) = 1 − Pr(C|x ) .
We randomly selected 2/3 of the computationally generated
C. Morimoto et al.
genotypes (including 166 collateral pairs and 166 lineal pairs for each
degree of kinship) as training datasets to build the logistic models using
the glm function in the R statistical language [18]. The remaining
genotypes (including 83 collateral and 83 lineal pairs for each degree of
kinship) were considered as test datasets. We calculated the Pr(C|x ) and
Pr(L|x ) of the test datasets from Eq. (1) and evaluated the accuracy and
false classification rate of the prediction model. Correct predictions
essentially represent instances for which the true relationship is equal
to the relationship with a higher probability. For example, when Pr(C|x )
is 0.6 and Pr(L|x ) is 0.4 in a collateral relative pair, the pair is correctly
classified as a collateral relationship. However, these probabilities do
not strongly support the collateral relationship in actual forensic case-
work. Therefore, we set three criteria of judgement for kinship de-
termination by including stricter criteria referring to the classical
Hummel’s predicates of paternity [19], as in our previous study [2]. The
criteria were as follows:
(1) a relationship is “supported” if the probability is ≥0.5,
(2) a relationship is “likely” if the probability is ≥0.9, and
(3) a relationship is “practically proven” if the probability is ≥0.998.
When both Pr(C|x ) and Pr(L|x ) were lower than the criterion, we
judged the relationship of the pair as “inconclusive” in the criterion of
(2) and (3).
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Forensic Science International: Genetics 33 (2018) 10–16
Fig. 2. Frequencies of ICS values in 249 computationally synthesized
familial genotypes of (a) second-degree relatives and (b) third-degree
relatives.
2.4. Validation using actual samples
To validate the prediction model, we used the SNP genotypes of
actual second-degree relative pairs and third-degree relative pairs
analyzed in our previous study [2]. These included 17 uncle–nephew
pairs, 17 grandfather–grandson pairs, 14 first cousin pairs, and two
great-grandfather–great-grandson pairs. These pairs were used regard-
less of sex because we targeted only autosomal SNPs. All participants
provided written informed consent, and this study was approved by the
Ethics Committee of the Graduate School of Medicine, Kyoto Uni-
versity. All samples were genotyped by using the HumanCore-12
BeadChip or HumanCore-24 BeadChip (Illumina), according to the
manufacturer’s protocol. We checked the genotyping quality from the
genotyping success rates by confirming that the rates were greater than
0.99, as recommended by the manufacturer to ensure good quality data.
From the genotypes of 174,254 SNPs, we investigated the number of
shared segments between each pair, as well as for the computationally
generated pairs. We then determined whether the pair has a collateral
relationship or lineal relationship by using our prediction models, si-
milar to the test datasets, and confirmed our prediction accuracy.
3. Results
3.1. Comparison of chromosomal sharing patterns between collateral and
lineal relatives
In the simulation data, the distributions of ICS values for the same
C. Morimoto et al.
Table 1
Median values of the mean and standard deviations (SDs) of the genetic lengths of shared
chromosomal segments among 249 simulated genotypes for each relationship.
Relationship mean (cM)
Uncle–nephew 30.5
Grandfather–grandson 47.0
First cousins 19.9
Great-grandfather–great-grandson 26.7
degree of kinship largely overlapped, as expected (Fig. 2). Therefore,
we could not distinguish collateral relatives from lineal relatives for the
same degree of kinship by using only ICS values. On the other hand,
there were large differences in the number of shared segments between
the uncle–nephew and grandfather–grandson pairs, despite the same
degree of kinship (Fig. 3a). The minimum, median, and maximum va-
lues for the uncle–nephew pairs were 47, 63, and 79, respectively.
These three quantiles were larger than the values for the grand-
father–grandson pairs (29, 39, and 53, respectively). Similarly, the
number of shared chromosomal segments in collateral relationships was
larger than that in lineal relationships with a third-degree of kinship
(Fig. 3b). The median values of the number of shared segments for first
cousins and great-grandfather–great-grandson kinships were 51 and 37,
respectively. From these results, the genetic length of each shared
Forensic Science International: Genetics 33 (2018) 10–16
Fig. 3. Frequencies of the number of shared segments in 249 com-
putationally synthesized familial genotypes of (a) second-degree re-
latives and (b) third-degree relatives.
segment in collateral relationships is expected to be shorter than that in
lineal relationships because the ICS values (the total genetic length of
the shared segments) are approximately identical for the same degree of
SD (cM) kinships. In fact, when we calculated the mean values and standard
deviations (SDs) of the genetic length of shared segments in each pair,
28.4 both values tended to be larger in lineal relationships than those in
47.0
collateral relationships with the same degree of kinship. We summar-
19.6
29.9 ized the means and SD values in each pair by using these medians
among 249 pairs in each relationship (Table 1).
3.2. Accuracy of the logistic regression model
By using the training datasets, we estimated β0 and β1 for the lo-
gistic regression model. In the second-degree relationship, β0 and β1
were −52.5 and 1.03, respectively. In the third-degree relationship, β0
and β1 were −24.0 and 0.557, respectively. Fig. 4 shows the logistic
curves and the number of shared segments in the training datasets
(boxplots) and indicates that the logistic models fitted the predicted
relationship.
We evaluated the accuracy of the prediction models by using the
test datasets (Table 2). About 80% of second-degree relatives had cor-
rectly predicted relationships, even when judged by the strictest cri-
terion (i.e., Pr(C|x ) or Pr(L|x ) ≥0.998). Third-degree relatives were
predicted with over 70% accuracy, as the criterion was ≥0.5 or ≥0.9.
13
C. Morimoto et al. Forensic Science International: Genetics 33 (2018) 10–16

Fig. 4. Logistic regression curves of the number of shared segments in

(a) second-degree relatives and (b) third-degree relatives. Gray and
white box plots show the training datasets for collateral and lineal
relationships, respectively.

Table 2 should select strict criteria, even if inconclusive results occur. In addi-
Prediction accuracy of the test datasets using three criteria. tion, when we tested the accuracy and false classification rates of the
training datasets, few differences were observed (Supplementary
Degree of kinship Criteria
Table 2).
≥0.5 ≥0.9 ≥0.998
3.3. Predicting relationships of actual samples
Second-degree 98.2% 95.2% 86.1%
Third-degree 94.0% 76.5% 22.9%
The genotyping success rates for all actual samples were > 0.99;
therefore, all data could be used for predicting relationships. The pre-
Table 3 diction accuracy of actual samples was similar to that of test datasets
False classification rates of the test datasets using three criteria. (Table 4). When we adopted a probability of ≥0.5, all samples were
judged as true relationships except for one first cousin pair. Because the
Degree of kinship Criteria
number of shared segments in this pair was 43, Pr(C|x ) and Pr(L|x ) were
≥0.5 ≥0.9 ≥0.998 0.479 and 0.521, respectively. Although these probabilities slightly
supported the hypothesis that the pair had a great-grandfather–great-
Second-degree 1.81% 0.602% 0% grandson relationship, we could not judge whether either relationship
Third-degree 6.02% 1.81% 0%
was “likely” using our criteria. Furthermore, when we adopted a
probability of ≥0.9 or ≥0.998, there was no false classification. These
However, it was difficult to distinguish first cousins from great-grand- results suggest that this method has a high ability for discriminating
parents–great-grandsons using the strictest criteria. However, false relationships with the same degree of kinship, especially second-degree
classification could be decreased because the criterion was stricter relationships.
(Table 3). Meanwhile, inconclusive results increased (e.g., 13.9% of
second-degree pairs and 77.1% of third-degree pairs, as the criterion 4. Discussion
was ≥0.998). To avoid incorrect determination in actual casework, we
We had previously proposed an approach for pairwise kinship

14
C. Morimoto et al.
Table 4
The number of actual sample pairs correctly determined using three criteria of judgement.
Relationship n* Criteria
≥0.5 ≥0.9
Uncle–nephew 17 17 15
Grandfather–grandson 17 17 14
First cousins 14 13 12
Great-grandfather–great-grandson 2 2 0 0
* n indicates the number of sample pairs.
analysis using ICS values calculated from high-density autosomal SNPs
[2]. In this study, we further developed this approach to distinguish
between collateral and lineal relationships with the same degree of
kinship. This method investigates chromosomal sharing patterns in
each relationship by counting the number of shared segments and
evaluates the relationship of the pair probabilistically from logistic re-
gression models. As expected, we determined that shared chromosomal
segments in collateral relationships with the same degree of kinship are
larger in number but smaller in genetic length than those in lineal re-
lationships. Therefore, these results suggest that the number of re-
combination events from the common ancestors influences chromo-
somal sharing patterns. We also validated the utility of our method by
using actual related samples from volunteers. Even when no predicted
relationship exists, such as in disaster victim identification, we can
determine the degree of kinship by using our previously published
approach [2], and then judge whether the relationship is collateral or
lineal using the method proposed in this study. Therefore, this method
is useful for identifying remains in forensic cases. However, in fact, the
final kinship determination of unidentified remains should be per-
formed in combination with other information (e.g., clothing, finger-
prints, skeleton morphological analysis, and dental records) [20].
Although uncalled events and genotyping errors rarely occurred in
high-density SNP genotyping systems, the number of shared segments
was seriously affected by the frequencies of these events. When we
ignored events for computationally generated genotypes, a discrepancy
between the number of shared segments in the simulation data versus
the actual sample data was observed (data not shown). We estimated
the probabilities of these events from the genotyping results of the
actual samples analyzed using DNA microarrays (i.e., HumanCore
BeadChip) and purposely added these events to synthesize realistic
genotypes. Moreover, if another genotyping system is used, we should
be able to estimate the probabilities depending on the quality of the
system.
In this study, we focused on two types of relationships: collateral
and lineal. In a certain degree of kinship, there is only one type of lineal
relationship (e.g., grandfather–grandson as a second-degree of kinship).
On the other hand, more than one type of collateral relationship exists
in the same degree of kinship. For example, half-siblings represent
collateral relationship with a second-degree of kinship. These re-
lationships, which have not been addressed in this study, may have
different chromosomal sharing patterns. Therefore, we need to evaluate
chromosomal sharing patterns for other relationships, to discern more
than two types of relationships.
Non-Japanese populations are expected to have different patterns of
chromosomal sharing regions. If this approach is applied to another
population, a large-scale SNP genotype dataset (i.e., > 1000 in-
dividuals) for the population will be needed to generate computer-
based families [2] and estimate the parameters in the logistic model.
Furthermore, we considered IBS regions longer than 4 cM as shared
chromosomal segments. However, we understand that these IBS regions
do not necessarily represent IBD regions. There are several methods for
rigorously estimating IBD regions using genome-wide SNP data
[21–25]. Therefore, these might improve the discrimination power
between each of these relationships.
Forensic Science International: Genetics 33 (2018) 10–16
In conclusion, this method allowed us to distinguish between col-
lateral relatives and lineal relatives with the same degree of kinship.
Therefore, our approach can be applied to kinship determination in-
volving personal identification. In the future, we plan to evaluate
≥0.998 whether the microarray typing system can be applied to degraded
forensic samples (e.g., nails, bones, or teeth).
15
13
5 Conflicts of interest
None.
Acknowledgments
We are grateful to the Nagahama Study Group. We also thank the
members of our laboratory for helpful discussions. This work was
supported by a Grant-in-Aid for JSPS Fellows (JSPS KAKENHI Grant
Number 17J07871).
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in the
online version, at http://dx.doi.org/10.1016/j.fsigen.2017.11.010.
References
[1] D.W. Gjertson, C.H. Brenner, M.P. Baur, A. Carracedo, F. Guidet, J.A. Luque,
R. Lessig, W.R. Mayr, V.L. Pascali, M. Prinz, P. Schneider, N. Morling, ISFG: re-
commendations on biostatistics in paternity testing, Forensic Sci. Int. Genet. 1
(2007) 223–231, http://dx.doi.org/10.1016/j.fsigen.2007.06.006.
[2] C. Morimoto, S. Manabe, T. Kawaguchi, C. Kawai, S. Fujimoto, Y. Hamano,
R. Yamada, F. Matsuda, K. Tamaki, Pairwise kinship analysis by the index of
chromosome sharing using high-density single nucleotide polymorphisms, PLoS
One 11 (2016) e0160287, http://dx.doi.org/10.1371/journal.pone.0160287.
[3] J. Goncalves, E. Conde-Sousa, T. Egeland, A. Amorim, N. Pinto, Key individuals for
discerning pedigrees belonging to the same autosomal kinship class, Forensic Sci.
Int. Genet. 29 (2017) 71–79, http://dx.doi.org/10.1016/j.fsigen.2017.03.018.
[4] N. Pinto, L. Gusmao, A. Amorim, X-chromosome markers in kinship testing: a
generalisation of the IBD approach identifying situations where their contribution is
crucial, Forensic Sci. Int. Genet. 5 (2011) 27–32, http://dx.doi.org/10.1016/j.
fsigen.2010.01.011.
[5] N. Pinto, P.V. Silva, A. Amorim, A general method to assess the utility of the X-
chromosomal markers in kinship testing, Forensic Sci. Int. Genet. 6 (2012)
198–207, http://dx.doi.org/10.1016/j.fsigen.2011.04.014.
[6] M. Kayser, Forensic use of Y-chromosome DNA: a general overview, Hum. Genet.
136 (2017) 621–635, http://dx.doi.org/10.1007/s00439-017-1776-9.
[7] E.A. Thompson, T.R. Meagher, Genetic linkage in the estimation of pairwise re-
lationship, Theor. Appl. Genet. 97 (1998) 857–864, http://dx.doi.org/10.1007/
s001220050965.
[8] M.P. Epstein, W.L. Duren, M. Boehnke, Improved inference of relationship for pairs
of individuals, Am. J. Hum. Genet. 67 (2000) 1219–1231, http://dx.doi.org/10.
1016/S0002-9297(07)62952-8.
[9] T. Egeland, N. Sheehan, On identification problems requiring linked autosomal
markers, Forensic Sci. Int. Genet. 2 (2008) 219–225, http://dx.doi.org/10.1016/j.
fsigen.2008.02.006.
[10] W.G. Hill, B.S. Weir, Variation in actual relationship as a consequence of Mendelian
sampling and linkage, Genet. Res. (Camb.) 93 (2011) 47–64, http://dx.doi.org/10.
1017/S0016672310000480.
[11] W.G. Hill, I.M. White, Identification of Pedigree Relationship from Genome Sharing,
G3 (Bethesda) 3 (2013) 1553–1571, http://dx.doi.org/10.1534/g3.113.007500.
[12] E.A. Thompson, Identity by descent: variation in meiosis, across genomes, and in
populations, Genetics 194 (2013) 301–326, http://dx.doi.org/10.1534/genetics.
112.148825.
[13] D. Speed, D.J. Balding, Relatedness in the post-genomic era: is it still useful? Nat.
Rev. Genet. 16 (2015) 33–44, http://dx.doi.org/10.1038/nrg3821.
[14] Z. Zeng, D.E. Weeks, W. Chen, N. Mukhopadhyay, E. Feingold, A pipeline for
classifying relationships using dense SNP/SNV data and putative pedigree in-
formation, Genet. Epidemiol. 40 (2016) 161–171, http://dx.doi.org/10.1002/gepi.
21948.
[15] O. Delaneau, J.F. Zagury, J. Marchini, Improved whole-chromosome phasing for
disease and population genetic studies, Nat. Methods 10 (2013) 5–6, http://dx.doi.
org/10.1038/nmeth.2307.
[16] The National Bioscience Database Center, The Nagahama Prospective Genome
Cohort for Comprehensive Human Bioscience, (2017) (Available:), https://
humandbs.biosciencedbc.jp/en/hum0012-v1.
[17] A.D. Johnson, R.E. Handsaker, S.L. Pulit, M.M. Nizzari, C.J. O’Donnell, P.I. de
Bakker, SNAP: a web-based tool for identification and annotation of proxy SNPs
using HapMap, Bioinformatics 24 (2008) 2938–2939, http://dx.doi.org/10.1093/
bioinformatics/btn564.
15
C. Morimoto et al.
[18] R.R. Core Team, A Language and Environment for Statistical Computing, R
Foundation for Statistical Computing, Vienna, Australia, 2017 (Available), http://
www.R-project.org/.
[19] K. Hummel, Biostatistical Opinion of Parentage, Stuttgart, Gustav Fischer Verlag,
1971 (written in German and English).
[20] M. Prinz, A. Carracedo, W.R. Mayr, N. Morling, T.J. Parsons, A. Sajantila,
R. Scheithauer, H. Schmitter, P.M. Schneider, DNA Commission of the International
Society for Forensic Genetics (ISFG): recommendations regarding the role of for-
ensic genetics for disaster victim identification (DVI), Forensic Sci. Int. Genet. 1
(2007) 3–12, http://dx.doi.org/10.1016/j.fsigen.2006.10.003.
[21] B.L. Browning, S.R. Browning, Improving the accuracy and efficiency of identity-by-
descent detection in population data, Genetics 194 (2013) 459–471, http://dx.doi.
org/10.1534/genetics.113.150029.
[22] S.R. Browning, B.L. Browning, Identity by descent between distant relatives:
16
Forensic Science International: Genetics 33 (2018) 10–16
detection and applications, Annu. Rev. Genet. 46 (2012) 617–633, http://dx.doi.
org/10.1146/annurev-genet-110711-155534.
[23] L. Han, M. Abney, Using identity by descent estimation with dense genotype data to
detect positive selection, Eur. J. Hum. Genet. 21 (2013) 205–211, http://dx.doi.
org/10.1038/ejhg.2012.148.
[24] C.D. Huff, D.J. Witherspoon, T.S. Simonson, J. Xing, W.S. Watkins, Y. Zhang,
T.M. Tuohy, D.W. Neklason, R.W. Burt, S.L. Guthery, S.R. Woodward, L.B. Jorde,
Maximum-likelihood estimation of recent shared ancestry (ERSA), Genome Res. 21
(2011) 768–774, http://dx.doi.org/10.1101/gr.115972.110.
[25] H. Li, G. Glusman, H. Hu, J. Shankaracharya, R. Caballero, D. Hubley,
S.L. Witherspoon, D.E. Guthery, L.B. Mauldin, L. Jorder, J.C. Hood, C.D. Roach,
Huff, Relationship estimation from whole-genome sequence data, PLoS Genet. 10
(2014) e1004144, http://dx.doi.org/10.1371/journal.pgen.1004144.